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Tag: minimap2
Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)
Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….
Maternal dominance contributes to subgenome differentiation in allopolyploid fishes
Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article CAS PubMed Google Scholar Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article PubMed Google Scholar Comai, L. The…
Pair ended short reads assemble to multiple references with a plasmid also inside
Pair ended short reads assemble to multiple references with a plasmid also inside 0 Hello, I am new to bioinformatics and am having trouble doing an assembly and alignment. First I will describe my sample data, I have Illumina MiSeq data of pair ended reads on a yeast organism. This…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
Topological structures and syntenic conservation in sea anemone genomes
Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article ADS CAS PubMed Google Scholar Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article ADS CAS PubMed PubMed Central Google Scholar Srivastava, M….
Why is the number of Minimap2 alignment observations different with CIGAR generation flag?
I am using Minimap2 in Linux to generate a sequence alignment between the Streptomyces coelicolor A3(2) chromosome (ref.fa) and the Mycobacterium tuberculosis chromosome (query.fa). My desired output is a PAF (Pairwise mApping Format) file. The general way to align reference and query sequences with Minimap2 is the following: minimap2 ref.fa…
ubuntu – Medaka: unrecognized command ‘tools’ and samtools not found
When trying to run medaka_consensus in ubuntu, I am getting the following error. I installed into a virtualenv to run on ubuntu. (medaka) ubuntu:~/medaka$ medaka_consensus -i combined.fastq -d curated.fasta -t -o ~/medaka 10 -m r941_sup_plant_g610 TF_CPP_MIN_LOG_LEVEL is set to ‘3’ [main] unrecognized command ‘tools’ Attempting to automatically select model version….
Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study
Kraemer, M. U. et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. Elife 4, e08347. doi.org/10.7554/eLife.08347 (2015). Article PubMed PubMed Central Google Scholar Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507. doi.org/10.1038/nature12060 (2013). Article ADS CAS PubMed PubMed Central …
Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files
Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files 0 Hi, Does anyone know if there’s an existing tool to calculate genetic distances between query and subject sequences in BAMs/SAMs? I’m reasonably sure it’s possible to identify transitions and transversions using data from the MD flag and the sequence, and…
Origin and evolution of the triploid cultivated banana genome
Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS PubMed PubMed Central Google Scholar Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…
r – Fst calculation from VCF files
I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and SNPs_s4.vcf, which contain information about SNPs. These vcf files were obtained by using the following methods: the initial input files were short-paired reads I did mapping with minimap2 ./minimap2 -ax sr ref.fa read1.fq.gz read2.fq.gz > aln.sam converted to bam file samtools…
vcfdist: accurately benchmarking phased small variant calls in human genomes
The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…
Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)
Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…
Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation
Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException 0 Hello, I’m attempting to create a test database with a smaller genome just to confirm I can get the pipeline running. I’m using PHG 1.8 with singularity. I was able to successfully run MakeDefaultDirectoryPlugin, CreateValidIntervalsFilePlugin, and MakeInitialPHGDBPipelinePlugin. Running AssemblyMAFFromAnchorWavePlugin yields an “IndexOutOfBoundsException” error, but the cause is…
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article ADS CAS Google Scholar Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…
Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs
Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
How to get unaligned reads and aligned reads into separate files from SAM/BAM? 0 I have long reads aligned with MiniMap2 in the form of SAM file. I want to get my unmapped reads into a file called unmapped.fastq.gz and my aligned reads into a file called mapped.fastq.gz. How can…
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article CAS PubMed Google…
A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei
Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…
2024 Co-Op, Bioinformatics job with Moderna, Inc.
The Roles: Exciting opportunities to work with Ph.D.-level computational biologists advancing Modernas mRNA therapeutics platform. This application covers three roles. Candidates with interest and skills fitting one or more of these are encouraged to apply. Our co-op program goes from: January 16th to June 14th 2024. All applicants must be…
MemVerge and Sentieon Announce WaveRider for Sentieon to Accelerate Next-Generation Sequencing in the Cloud
Early Customers Realize 10x Increase in Performance and Cloud Cost Savings; Sentieon Software Offered Free in Memory Machine Cloud Subscription MILPITAS, Calif., Nov. 14, 2023 /PRNewswire/ — MemVerge®, pioneers of Big Memory software, and Sentieon®, the market leader in genomics software, today announced a collaboration to accelerate next-generation sequencing (NGS)…
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article CAS PubMed Google Scholar Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…
how to count the number of reads align per viruses in my sample
how to count the number of reads align per viruses in my sample 3 Hello, I would like to count the number of reads aligning per viruses in my sample based on the output of minimap2 in a bam file. Does anyone how to proceed? By using the command: samtools…
Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly
Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly 0 We have two groups sample of yeast species, control (1 sample) and treatment (1 sample), whose complete reference genome isn’t available yet to do alignment nor variant calling. The objective of this project is straightforward, simply wanting to…
Chimeric alignment with minimap2
Chimeric alignment with minimap2 1 Hi, On minimap2 github (github.com/lh3/minimap2) it says : For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply…
Strand bias in supplementary alignments from Nanopore
Strand bias in supplementary alignments from Nanopore 0 I have nanopore reads for Leishmania major aligned with minimap2. I observe an odd strand bias in the supplementary alignments in that segments aligning on forward strand are more represented than reverse aligning segments (7601 vs 6396 or 54% vs 46%). For…
Chromosome-level genomes of three key Allium crops and their trait evolution
Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article Google Scholar Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….
bash – Racon: empty overlap set!
Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then converted from bam to fastq using samtools, then trimmed using nanofilt from there…
minimap2 error while running TrinityFusion
I have followed the steps you outlined previously, but I’m encountering errors with both methods, whether I’m using Singularity or running it locally. COMMAND USED FOR MOUNTING: singularity exec -e -B /home/sklab/simran/star_run/library/ctat_genome_lib_build_dir/:/ctat_genome_lib trinityfusion.v0.4.0.simg /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion –prep_reference_only -T long_read.fastq(fake)–genome_lib_dir /home/sklab/simran/star_run/library/ctat_genome_lib_build_dir/ COMMAND USED FOR RUNNING SAMPLE: singularity exec -e -B ~/simran/star_run/library/ctat_genome_lib_build_dir/:/ctat_genome_lib_build_dir…
samtools view problems when extracting subset of fastq – usegalaxy.eu support
After using Minimap2 on a set of nanopore reads aligning them to the contigs from a Flye assembly to produce a Bam file (about 30 Gb) I now identified contamination and have a subset of contigs I want to use to extract the Fastq files that align to these contigs…
Adversarial and variational autoencoders improve metagenomic binning
Overview of AAMB The AAMB workflow consists of the following main steps (Fig. 1a). First, Tetra Nucleotide Frequencies (TNF) and per sample co-abundances (Coab) are extracted from the contigs and BAM files of reads mapped to contigs, and input to the AAMB model as a concatenated vector. The AAMB model encodes…
Visualize raw rna fastq file and aligned bam file
Visualize raw rna fastq file and aligned bam file 1 Hi, I am trying to see how raw rna fasq and aligned bam file look like by any visualization tools. Are there any tools to visualize fastq files? Furthermore, are there any tools to see what the mapped bam file…
Disease-specific loss of microbial cross-feeding interactions in the human gut
Wang, T., Goyal, A., Dubinkina, V. & Maslov, S. Evidence for a multi-level trophic organization of the human gut microbiome. PLOS Comput. Biol. 15, e1007524 (2019). Article ADS PubMed PubMed Central Google Scholar Fischbach, M. A. & Sonnenburg, J. L. Eating for two: how metabolism establishes interspecies interactions in the…
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article Google Scholar Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….
Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
Ceballos, G., Ehrlich, P. R. & Raven, P. H. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction. Proc. Natl Acad. Sci. USA 117, 13596–13602 (2020). Article CAS PubMed PubMed Central Google Scholar Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the…
How would you define homologous windows between 2 genomes?
How would you define homologous windows between 2 genomes? 0 Hello, Let’s say I have genome A and genome B, each of a single chromosome. How would you define homologous windows between the two? What I can think of is 1) mapping with minimap2 the 2 chromosomes 2) look at…
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …
fastq – Parameter optimisation of minimap2
I’m leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files. minimap –heap-sort=yes –splice-flank=no metagenome.fastq.gz fastaDB.fas What I noticed is the low tolerance of mismatch when I need to maximise mismatch because microbes have loads of genetic diversity. Thus the collection of references sequences are never really…
Identification of herpesvirus transcripts from genomic regions around the replication origins
Roizman, B. Herpes Simplex Viruses. In Fields Virology (Lippincott Williams & Wilkins, 2013). Google Scholar Deluca, N. A., Mccarthy, A. M. & Schaffer, P. A. Isolation and characterization of deletion mutants of herpes simplex virus type 1 in the gene encoding immediate-early regulatory protein ICP4. J. Virol. 56, 558–570 (1985)….
Recommendations for extending contigs from denovo assembly to identify SV insertion sites on chromosome
I performed WGS of a new transgenic mouse model generated by random integration of a 10.316Kb transgene with the goal of locating the insertion site/s and calculating copy-number. The PromethION flowcell produced an output of 54.86Gb with 2.37 Million reads generated and I received this data in the form of…
Scaling logical density of DNA storage with enzymatically-ligated composite motifs
Composite motifs as building blocks for DNA storage A composite motif is a representation of a position in an oligo sequence that uses a combination of motifs drawn from a fixed motif library to encode data. For example, assuming a library of 32 motifs, and a combination factor of four,…
Scalable GPU Implementation of Minimap2 for Long Read Alignment
Download PDFOpen PDF in browser EasyChair Preprint no. 10935 7 pages•Date: September 21, 2023 Abstract Minimap2 is a widely-recognized tool for long read alignment, known for its speed and precision. In this article, we explore how Graphics Processing Units (GPUs) can be harnessed to accelerate Minimap2, enhancing the efficiency and…
Accelerating Minimap2 for Accurate Long Read Mapping on Graphics Cards
Download PDFOpen PDF in browser EasyChair Preprint no. 10932 4 pages•Date: September 21, 2023 Abstract Minimap2, a versatile tool for long read alignment, has gained prominence for its speed and precision. In this article, we explore how Graphics Processing Units (GPUs) can be harnessed to accelerate Minimap2, enhancing the efficiency…
Fast and robust metagenomic sequence comparison through sparse chaining with skani
Sequence identity estimation Formally, let G be a string of nucleotides and \({G}^{{\prime} }\) be a mutated version of G where every letter is independently changed to a different letter with probability θ. We will define the true ANI to be equal to 1 − θ under our model. Under the usual…
mRNA vaccine quality analysis using RNA sequencing
Design and synthesis of reference plasmid A reference construct was first designed, with the intention of optimising the production of RNA therapeutics for pre-clinical research. The coding sequence of eGFP30 was selected as a reporter in the coding region, as its protein product can be assayed simply through Flow cytometry…
Recommended order of operations for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
I generated a new transgenic mouse through random multi-copy integration of a 10.316 Kb DNA fragment with a known sequence . We performed WGS using the PromethION flow cell. From the core I received 500+ fastq files that I have subsequently merged. So far I have performed: de novo assembly…
The Impact of Harisankar Sadasivan’s Research in Revolutionizing Healthcare through Computer System Design
Over the past few years, the healthcare sector has undergone a profound transformation, characterized by the emergence of innovative business models, unexpected partnerships, and a heightened need for efficiency. The conventional pace of digital adoption within healthcare had often lagged behind other industries, but the pandemic acted as a catalyst,…
GPU-Enhanced Minimap2 for Precise Long Read Alignment
Download PDFOpen PDF in browser EasyChair Preprint no. 10914 3 pages•Date: September 16, 2023 Abstract Minimap2 is a widely-used tool for long read alignment, known for its speed and sensitivity. However, the alignment of long reads to reference genomes can still be computationally intensive. In this article, we explore the…
minimap2-sys 0.1.16+minimap2.2.26 – Docs.rs
Use this if you need lower-level bindings for minimap2. Also works with mm2-fast. Currently this is synced to a recent git commit of minimap2. If you have other needs, let me know and I can make a branch and publish a corresponding version. Features vendored – Regenerate the bindings from…
Feature flags of minimap2-sys crate // Lib.rs
Cargo Features [dependencies] minimap2-sys = { version = “0.1.15+minimap2.2.26”, default-features = false, features = [“vendored”, “noopt”, “zlib-ng”, “static”] } default These default features are set whenever minimap2-sys is added without default-features = false somewhere in the dependency tree. Enables libc of libz-sys vendored = bindgen mm2-fast sse2only simde noopt zlib-ng…
Molecular detection and characterization of SARS-CoV-2 in cats and dogs of positive owners during the first COVID-19 wave in Brazil
Study design This was an observational study conducted between October 2020 and June 2021 in five large metropolitan areas in Brazil, belonging to four of the five different Brazilian geographical regions (Recife, Belo Horizonte, São Paulo, Campo Grande and Curitiba). Dogs and cats whose owners tested positive for SARS-CoV-2 by…
Which minimap2 parameters to set while performing mapping to avoid such mismatches
Which minimap2 parameters to set while performing mapping to avoid such mismatches 1 Hi all, Apologies that I don’t have a lot of experience with this stuff, but It’s been a long time since I am struggling with this issue. I am aligning my RNA seq data of a heterologous…
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article ADS CAS PubMed Google Scholar Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …
Moderna hiring 2024 Co-Op, Bioinformatics in Cambridge, Massachusetts, United States
The Roles:Exciting opportunities to work with Ph.D.-level computational biologists advancing Moderna’s mRNA therapeutics platform. This application covers three roles. Candidates with interest and skills fitting one or more of these are encouraged to apply.Our co-op program goes from: January 16th to June 14th 2024. All applicants must be available for…
The GATK “The given bam input has no sample names.” error
The GATK “The given bam input has no sample names.” error 1 for f in MINIMAP BWA ; do ~/gatk-4.2.0.0/gatk HaplotypeCaller –reference /home/tmichel/projects/rbge/HybSeq_thibauld/reference_genomes/Begonia_loranthoides_scaffold.fasta –input Hillebrandia_sorted.$f.bam –output Hillebrandia.$f.g.vcf.gz –emit-ref-confidence GVCF ; done I have used GATK to call variants in BAM files files with both minimap2 and bwa mem with the…
Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing | BMC Infectious Diseases
Pappas G, Papadimitriou P, Akritidis N, Christou L, Tsianos EV. The new global map of human brucellosis. Lancet Infect Dis. 2006;6(2):91–9. Article PubMed Google Scholar Pappas G. The changing Brucella ecology: novel reservoirs, new threats. Int J Antimicrob Agents. 2010;36(Suppl 1):8–11. Article Google Scholar Wyatt HV. Lessons from the history…
How to get the species abundance in metagenomic data sequenced by PacBio/Nanopore?
How to get the species abundance in metagenomic data sequenced by PacBio/Nanopore? 0 Hello Experts, I am working with some microbial metagenomic data. As the third-generation sequencer be come more famous. I wonder if there is any method to get the species abundance in metagenomic data sequenced by PacBio or…
What are bitsets in Samtools flagstat output?
What are bitsets in Samtools flagstat output? 0 Hello, I am am trying to use Samtools flagstat to analyze my BAM file after aligning nanopore dRNAseq reads to a reference transcriptome using minimap2. The output file indicates I have the following flagstats below (excluded zero values from output). 729779 +…
How to find the coverage of the assembled contigs of the PacBio long reads?
How to find the coverage of the assembled contigs of the PacBio long reads? 1 Hi, I have assembled the 3-cells reads data of PacBio HiFi. Question is how can I find the coverage of my assembled contigs? I shall be grateful to you. PacBio assembly coverage • 48 views…
Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism
Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…
Minimap2 map-pb index for ONT reads
Minimap2 map-pb index for ONT reads 1 Hi! I made a minimap2 index for a custom genome. I was planning on using it for pacbio and nanopore data. I created the index using minimap2 -x map-pb -d genome.mmi genome.fa. Unfortunately, I forgot to make one specifically for the nanopore data…
Investigating open reading frames in known and novel transcripts using ORFanage
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar Pertea,…
Rapid gene content turnover on the germline-restricted chromosome in songbirds
This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…
How to liftover SNP positions from one genome to another genome?
How to liftover SNP positions from one genome to another genome? 1 Hello, Do you know a good way to map contigs/snp-regions from one genome to another? At the moment, I would like to check the positions of the SNPs that I obtained from one reference genome on the new…
Comparative studies of X chromosomes in Cervidae family
Prothero, D. R. et al. On the unnecessary and misleading taxon “Cetartiodactyla”. J. Mamm. Evol. 29, 93–97. doi.org/10.1007/s10914-021-09572-7 (2022). Webb, S. D. Evolutionary history of new world Cervidae. In Antelopes, Deer, and Relatives: Fossil Record, Behavioral Ecology, Systematics, and conservation (eds. Vrba, E. & Schaller, G.) 38–64 (Yale University Press,…
Processing Fast5 files from ONT for direct RNA
Processing Fast5 files from ONT for direct RNA 2 Hi, Am trying to process some sequencing data from ONT. I have fast5, fastq, fasta files. I have also generated bam files with minimap2 and samtools. However, when I cam trying to run Nanopolish, ELIGOS2, DRUMMER, Tombo – all tools are…
Isolation and genome characterization of Lloviu virus from Italian Schreibers’s bats
Ethics and biosafety statement Bats were captured during the day with hand-nets in full compliance with best practice and national and European regulations, in derogation to the Council Directive 92/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora (authorization 38,025 of 13/08/2020…
The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation
Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article Google Scholar Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…
Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor
Crutzen, P. J. The influence of nitrogen oxides on the atmospheric ozone content. Q. J. R. Meteorol. Soc. 96, 320–325 (1970). Article Google Scholar Johnston, H. Reduction of stratospheric ozone by nitrogen oxide catalysts from supersonic transport exhaust. Science 173, 517–522 (1971). Article CAS PubMed Google Scholar Hughes, M. N….
Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities
Rantanen M, Karpechko AY, Lipponen A, Nordling K, Hyvärinen O, Ruosteenoja K, et al. The Arctic has warmed nearly four times faster than the globe since 1979. Commun Earth Environ. 2022;3:1–10. Article Google Scholar Kwok R. Arctic sea ice thickness, volume, and multiyear ice coverage: losses and coupled variability (1958–2018)….
Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling
Albertsen, M. Long-read metagenomics paves the way toward a complete microbial tree of life. Nat. Methods 20, 30–31 (2023). Article CAS PubMed Google Scholar van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. years of next-generation sequencing technology. Trends Genet. 30, 418–426 (2014). Article PubMed Google Scholar …
No Sequence Segments for secondary alignments in minimap2 while trying to run alignment on ONT data?
No Sequence Segments for secondary alignments in minimap2 while trying to run alignment on ONT data? 0 Hello all, I was trying to align a set of ONT reads that I have against my reference and I noticed something strange in the generated SAM file. If a read has any…
Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons
Clinical RNA SARS-CoV-2 isolate For surveillance studies, a set of residual nasopharyngeal swab specimens positive for SARS-CoV-2 qRT-PCR from the Republican Diagnostic Centre (RDC) (umc.org.kz/en/) and private laboratory KDL “Olymp” (www.kdlolymp.kz/) were collected across the Republic of Kazakhstan between 2020 and 2022. 341 sequences that passed quality control are deposited…
Batch correction for Nanopore RNAseq
Batch correction for Nanopore RNAseq 0 I have 3 RNAseq experiments that were sequenced on a MinION and I am trying to do some differential expression analysis with them. This is my pipeline: Basecalling with Guppy Cleaning using chopper Aligning to the genome (mouse) with minimap2 Counting using featureCounts At…
Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe
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A complete telomere-to-telomere assembly of the maize genome
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Applications of long-read sequencing to Mendelian genetics | Genome Medicine
Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, et al. A randomized, controlled trial of the analytic and diagnostic performance of singleton and trio, rapid genome and exome sequencing in ill infants. Am J Hum Genet. 2019;105(4):719–33. Article CAS PubMed PubMed Central Google Scholar Costain G,…
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….
A pangenome reference of 36 Chinese populations
Populations and samples For Phase I of the CPC project, we selected 68 samples from 731 individuals with genomes deep-sequenced using next-generation sequencing. Following a previous study5, we applied a procedure to quantitatively evaluate the genetic diversity coverage based on principal component analysis results. We selected individuals using a statistic…
Integrated multi-omics for rapid rare disease diagnosis on a national scale
Ethics The Australian Genomics Acute Care study has Human Research Ethics Committee approval (HREC/16/MH/251). Parents provided informed consent for participation in the study, following genetic counseling. Study design and participants The Acute Care Genomics program is a national multi-site study delivering ultra-rapid genomic testing to critically ill pediatric patients with…
Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil
Study sites Soils were collected from two different sites (ARDEC: Colorado State University’s Agricultural Research, Development and Education Center in Fort Collins, CO; and CPCRC: USDA Columbia Plateau Conservation Research Center in Pendleton, OR). At each site, four replicate plots of no-till corn (ARDEC) or no-till annual wheat (CPCRC) were…
Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors
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Gap-free genome assembly of anadromous Coilia nasus
Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS Google Scholar Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…
minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping
Abstract minimap2 is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. While minimap2 is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we present minimap2-fpga, a hardware-accelerated version of minimap2 that speeds up the mapping process by integrating…
Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases | Human Genomics
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Illumina Complete Long Reads software analysis workflow for human WGS
Introduction Next-generation sequencing (NGS) enables scientists to decipher the genome for a deeper understanding of biology. Proven Illumina sequencing by synthesis (SBS) chemistry combined with award-winning DRAGEN secondary analysis delivers whole-genome sequencing (WGS) data with outstanding accuracy.1,2 DRAGEN Multigenome (graph) further improves mapping accuracy in challenging regions by ~50%.1 Still,…
Impute haplotypes (ImputePipelinePlugin) execution error
Impute haplotypes (ImputePipelinePlugin) execution error – PHG 1 Hi there, I am trying to get my PHG imputation pipeline running. I use a small reference panel and a large low-coverage nested population to be imputed. The first part of the pipeline run properly, creating the pangenome.fa, aligning the read using…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article ADS CAS PubMed Google Scholar Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article Google Scholar Darwin, C. The Descent of Man, and Selection…
Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
Bessant, D. A., Ali, R. R. & Bhattacharya, S. S. Molecular genetics and prospects for therapy of the inherited retinal dystrophies. Curr. Opin. Genet. Dev. 11, 307–316 (2001). Article CAS PubMed Google Scholar Berger, W., Kloeckener-Gruissem, B. & Neidhardt, J. The molecular basis of human retinal and vitreoretinal diseases. Prog….
NanoSim Error “Please specify the training reads and its reference genome!”
NanoSim Error “Please specify the training reads and its reference genome!” 1 Hi, I installed nanosim using conda install -c bioconda nanosim and then tried to run the read characterization using read_analysis.py transcriptome -i training_reads.fastq -r reference_genome.fa -rt reference_transcriptome.fa -annot reference_annotation.gtf -o training. However, I get the following error: Please…
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Cutler, E. B. The Sipuncula: Their Systematics, Biology, And Evolution (New York: Cornell University Press, doi.org/10.7591/9781501723643, 1994) Nielsen, C. Some aspects of spiralian development. Acta Zool. 91, 20–28, doi.org/10.1111/j.1463-6395.2009.00421.x (2010). Article Google Scholar Huang, D. Y., Chen, J. Y., Vannier, J. & Saiz Salinas, J. I. Early Cambrian sipunculan worms…
interpreting inversions on IGV
interpreting inversions on IGV 1 I just started working with PacBio and Nanopore long reads, after some preliminary QCing I mapped the reads using minimap2. I am looking at the inversions for now and I have igv images for one of my regions. I want to know is it how…
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…
Ancient gene linkages support ctenophores as sister to other animals
Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article PubMed PubMed Central Google Scholar Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…
BBmap params for accurate MAG relative abundance estimation?
hi folks, Recently, I’ve been working on developing molecular and computational methods to improve the accuracy of relative abundance estimation of metagenome assembled genomes (MAGs) from NGS datasets. Most of this work is focused on host-associated viral metagenomics, where quite a bit of nucleic acid manipulation and amplification is needed…
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
Ethics statement All experiments with hamsters were performed in accordance with the Science Council of Japan’s Guidelines for the Proper Conduct of Animal Experiments. The protocols were approved by the Institutional Animal Care and Use Committee of National University Corporation Hokkaido University (approval ID: 20-0123 and 20-0060). All protocols involving…