Tag: minimap2
Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors
Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article Google Scholar El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…
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
Hingorani M, Hanson I, van Heyningen V. Aniridia. Eur J Hum Genet. 2012;20:1011–7. Article CAS PubMed PubMed Central Google Scholar Lima Cunha D, Arno G, Corton M, Moosajee M. The spectrum of PAX6 mutations and genotype-phenotype correlations in the eye. Genes. 2019;10:1050. Article PubMed PubMed Central Google Scholar Cvekl A,…
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…
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Figure 1 shows the detailed workflow of the study. Fig. 1 General overview of the study. Briefly, MPXV was isolated from a skin lesion and then was used to infect CV-1 cells. After the designated infection times, total RNA was isolated and sequenced using direct cDNA sequencing protocol on ONT’s MinION platform….
GraphAligner/vg surject – alignment output nonsense?
GraphAligner/vg surject – alignment output nonsense? 0 Following on from some advice I received in a previous post, I’ve attempted to use GraphAligner and vg surject to map long reads to the T2T reference genome, and it seems to be resulting in nonsense outputs – a much smaller BAM than…
Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing | Virology Journal
Targeted amplicon paneling and nanopore sequencing A set of primer pools, protocols, and computational commands were designed to sequence hMPXV1 genomes on a MinION nanopore flow cell (Fig. 2A). All necessary protocols are briefly described in the Methods section and available as Additional file 2: Working Laboratory Protocols. Initial amplicon primers…
Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus
Ethics declaration Animal study was performed following the Guide for the Care and Use of Laboratory Animals. Animal experiment was approved by the Institutional Animal Care and Use Committee of Colorado State University (protocol number 1090) in advance and conducted in compliance with the Association for the Assessment and Accreditation…
RNA SEQ reads assembly for illumina sequenced data
RNA SEQ reads assembly for illumina sequenced data 0 Hi, everyone, I have 10 samples paired end . I have done the quality check and trimming then I merged the trimmed reads and after that I have done the mapping using minimap2. using this command . minimap2 -ax map-ont ref.fna(reference…
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
Sagan, L. On the origin of mitosing cells. J. Theor. Biol. 14, 225 (1967). Article ADS CAS Google Scholar McBride, H. M., Neuspiel, M. & Wasiak, S. Mitochondria: More than just a powerhouse. Curr. Biol. 16, R551–R560 (2006). Article CAS PubMed Google Scholar Dietrich, M. O., Liu, Z.-W. & Horvath,…
How to convert SAM/BAM file to GTF/GFF file?
How to convert SAM/BAM file to GTF/GFF file? 1 Hello, Curious to know if there’s a way to convert SAM/BAM file generated using minimap2 to GTF/GFF file. The purpose is to use it as transcript alignment evidence for EVM. Kindly suggest! Regards, B GTF SAM BAM GFF minimap2 • 32…
An apicomplexan parasite drives the collapse of the bay scallop population in New York
Lafferty, K. D., Porter, J. W. & Ford, S. E. Are diseases increasing in the ocean?. Ann. Rev. Ecol. Evol. Syst. 35, 31–54 (2004). Article Google Scholar Ward, J. R. & Lafferty, K. D. The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing?. PLoS Biol. 2, 542–547…
TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication
Cell lines and tissue culture The murine 17-CL1 cell line (derived from 3T3 cells, BEI Resources, Cat. No. NR-53719) was maintained in Dulbecco Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The NCTC clone 1469 cell line…
Expected number of haplotype IDs per path in PHG
Expected number of haplotype IDs per path in PHG 0 Hello! I have recently managed to run the Pathfinding step of the Practical Haplotype Graph pipeline (see here; PHG v1.4). With this I now wanted to get the calculated best path, i.e. the list of haplotype IDs that are part…
Overlap File for RACON Genome Polisher
Overlap File for RACON Genome Polisher 0 This seems like a dumb question, but I have no idea how to generate an overlap file that is required for RACON. According to the documentation: github.com/isovic/racon Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and…
Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge
Baumgart, D. C. & Sandborn, W. J. Inflammatory bowel disease: Clinical aspects and established and evolving therapies. Lancet 369(9573), 1641–1657 (2007). Article CAS PubMed Google Scholar Baumgart, D. C. The diagnosis and treatment of Crohn’s disease and ulcerative colitis. Deutsches Aerzteblatt Online 106(8), 123–133 (2009). Google Scholar Conrad, K., Roggenbuck,…
how to choose an efficient filtering threshold to remove shorter and low quality reads before doing alignment of Nanopore long reads
how to choose an efficient filtering threshold to remove shorter and low quality reads before doing alignment of Nanopore long reads 0 I just started processing ONT long reads which obtained from soft tissue sarcomas. I have a very general question, what would be an ideal filtering threshold for read…
The little skate genome and the evolutionary emergence of wing-like fins
Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article ADS CAS PubMed PubMed Central Google Scholar Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….
Mutation-induced infections of phage-plasmids | Nature Communications
Media The minimal marine media, MBL media, was used for serial dilution growth of Tritonibacter mobilis A3R06. It contained 10 mM NH4Cl, 10 mM Na2HPO4, 1 mM Na2SO4, 50 mM HEPES buffer (pH 8.2), NaCl (20 g/liter), MgCl2*6H2O (3 g/l), CaCl2*2H2O (0.15 g/l), and KCl (0.5 g/l). Glucose was added as the only carbon source at a…
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article CAS PubMed Google Scholar Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS PubMed PubMed Central Google Scholar Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS PubMed Google Scholar Peralta, I. E., Spooner, D. M. & Knapp, S….
how can i filter a sam file from a paf file
how can i filter a sam file from a paf file 1 I used minimap2 to produce an alignment and I outputted it into 2 formats, .paf and .sam. I did some filtering on the .paf version and now I would like to filter the alignments in the .sam file…
Best way to visualize .paf or .sam alignment to a fasta file
Best way to visualize .paf or .sam alignment to a fasta file 0 I recently wanted to see how a bunch of contigs align to a telomere to telomere genome assembly so I used minimap2 to align them and now I have 2 alignment files, one as a.paf file and…
Accelerating Minimap2 for Accurate Long Read Alignment on GPUs
doi: 10.26502/jbb.2642-91280067. Epub 2023 Jan 20. Affiliations Expand Affiliations 1 Department of Computer Science and Engineering, University of Michigan Ann Arbor, MI 48109, USA. 2 NVIDIA Corporation, Santa Clara, CA 95051, USA. Free PMC article Item in Clipboard Harisankar Sadasivan et al. J Biotechnol Biomed. 2023. Free PMC article Show details…
Minimap2 giving opposite strand orientation than Pychopper
Minimap2 giving opposite strand orientation than Pychopper 0 Hello! We sequenced cDNA using nanopore technology. I used Pychopper to orient my reads before mapping them to the human reference genome. However, when after the reads are mapped, many of them are the opposite orientation as predicted by pychopper. Why could…
Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements
Morelli, L. & Capurso, L. FAO/WHO guidelines on probiotics: 10 years later. J. Clin. Gastroenterol. 46, S1–S2 (2012). Article PubMed Google Scholar Arsène, M. M. J. et al. The use of probiotics in animal feeding for safe production and as potential alternatives to antibiotics. Vet World 14, 319–328 (2021). Article …
minimap2 – Extracting positions from PAF files in order to extract sequences from a Fastq file with Python
I have used Minimap2 to create a paf file by aligning a Fastq file against itself. Now from this Paf file I can see where the reads overlap, and I want to take these positions, and use them to extract the entire sequences between these positions from the paf file…
PHG -imputeTarget pathToVCF plugin not writing expected output files?
Hello! I am trying to do the last few steps of the Practical Haplotype Graph pipeline as described here . I am running PHG v1.2, have loaded the Haplotypes to the database, created the pangenome fasta and am now trying to impute the best paths for different samples using WGS…
Filtering mapping results by percent identity and aligned percent?
Filtering mapping results by percent identity and aligned percent? 0 Can we filter results of mapping tools by percent-identity and aligned-percent? And, is conducting such filtering appropriate? I thought that mapping tools like minimap2, bowtie2 or bwa-mem didn’t have such options, but I found that COVERM, that conduct both mapping…
bwa-mem2 vs htslib – compare differences and reviews?
What are some alternatives? When comparing bwa-mem2 and htslib you can also consider the following projects: minimap2 – A versatile pairwise aligner for genomic and spliced nucleotide sequences bowtie2 – A fast and sensitive gapped read aligner genozip – A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF,…
Transcript feature coverage with coverage of each feature shown like e.g. UTR’s CDS, exons etc
Transcript feature coverage with coverage of each feature shown like e.g. UTR’s CDS, exons etc 0 Hi, We are all familiar with rseqc genebody coverage functions rseqc.sourceforge.net/#genebody-coverage-py. But I was wondering if there is an existing implementation of transcript level coverage with each of the features of transcript (like 5’UTR,…
Benefit of running pathfinding for all samples together or individually?
Benefit of running pathfinding for all samples together or individually? 0 Hello, Thank you for your continuous help so far! I was wondering if there is there is a benefit to running the pathfinding through the PHG for all samples I have together or if it does not matter much?…
Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae
Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article CAS Google Scholar Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …
how to convert minimap2 generated sam file to bam
how to convert minimap2 generated sam file to bam 1 I have mapped the reference chromosome assembly on other chromosome assemblies using minimap2 to generate sam file. my sam file doesn’t have header I tried samtools ref.fa.fai sample.sam sample.bam and samtools view -bT ref.fa sample.sam > sample.bam both errors are:…
Can’t add read group correctly to minimap2 sam alignmnet
Can’t add read group correctly to minimap2 sam alignmnet 1 Hello I am running minimap2 in a pipeline with GATK that needs read group data @RG with sample information. minimap2 -ax sr -t 20 -I 100G -R @RG\\tID:A00253_251_HTN2JDSXY.2\\tPL:ILLUMINA\tLB:LB1\\tSM:TA90 ref.mmi reads_1.fq.gz reads_2.fq.gz | samtools view -bh -F 260 -T ref.fa >out.bam…
Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA
Walker, M. J. et al. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin. Microbiol. Rev. 27, 264–301 (2014). Article PubMed PubMed Central Google Scholar Carapetis, J. R., Steer, A. C., Mulholland, E. K. & Weber, M. The global burden of group A streptococcal diseases. Lancet Infect. Dis. 5,…
Build multi-arch images with different commands per architecture in Docker file – General Discussions
mcrotti1 (Mcrotti1) February 24, 2023, 10:24am 1 Hello, I have a question related to building containers for multi architectures.I am working from a mac the the M1 arm chip. Usually, I write my docker file and use the commanddocker buildx build –platform linux/arm64,linux/amd64 -t name:latest –push .And this works fine,…
Fellowships Job: Postdoctoral Research Fellow in Bioinformatics/Computational Biology
Job ID: 27118 Location: 450 Brookline Ave, Boston, MA 02215 Category: Fellowships Employment Type: Full time Work Location: Onsite:Up to 1 day remote/wk Overview Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of…
Structural variants identified from same reads / assembly
Structural variants identified from same reads / assembly 0 Hello, I did an assembly with Pacbio Hifi reads. The metrics are very well. I decided to do a SV calling with pbsv tool : I aligned the initial reads on this assembly with minimap2 , and I detected many SVs…
Pacbio de-novo assembly
Pacbio de-novo assembly 2 Hi,Recently I got Pacbio Hifi reads generated using CCS mode of a plant whole genome de-novo assembly.I received 2 file types from the sequencing facility.Fastq.gz and Bam fileI am getting confused in two places. From my understanding i learned that Pacbio sequencing output is in bam…
Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects | Parasites & Vectors
Pérez de León AA, Mitchell RD, Watson DW. Ectoparasites of cattle. Vet Clin North Am Food Animal Prac. 2020;36:173–85. Article Google Scholar Gómez-Díaz E, Figuerola J. New perspectives in tracing vector-borne interaction networks. Trends Parasitol. 2010;26:470–6. Article PubMed Google Scholar Kent RJ. Molecular methods for arthropod bloodmeal identification and applications…
Can ARIBA AMR tool be tweaked to support long reads inputs (eg-Oxford Nanopore)?
Can ARIBA AMR tool be tweaked to support long reads inputs (eg-Oxford Nanopore)? 0 Hi, As my master thesis project, I was wondering if I could tweak the AMR finding tool ARIBA pipeline to accept long read as input. I could not find any useful resources related to that. My…
Clarification on the usage of pangenomeHaplotypeMethod/pathHaplotypeMethod
Clarification on the usage of pangenomeHaplotypeMethod/pathHaplotypeMethod 0 Hello! I am currently trying to impute paths through a built Practical Haplotype Graph, i.e. use the -ImputePipelinePlugin -imputeTarget command. The PHG version I use is 1.2. I populated the database using assemblies and the built-in anchorwave plugin. I have fastq files as…
Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains
This research complies with all relevant ethical regulations approved by the Human Investigation Review Board of Albert Szent-Györgyi Clinical Centre of the University of Szeged and the National Biodiversity Authority (NBA) of India. Permission for the faecal sample collection was obtained from the Human Investigation Review Board of Albert Szent-Györgyi…
How I know the genome assembly quality by the low coverage Pacbio data ?
How I know the genome assembly quality by the low coverage Pacbio data ? 0 Hi, I have finished the assembly genome, and i have a low average Pacbio data. I want to estimate the quality of the result. So, i map the Pacbio data to the aseembly genome by…
Cost-effective and accurate genomics analysis with Sentieon on AWS
This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…
How to compare a Nanopore read (.fastq) to a genome assembly file (.fna)
How to compare a Nanopore read (.fastq) to a genome assembly file (.fna) 0 Hi, I want to compare a Nanopore read in fastq format to a reference genome file of an animal in fna format in order to determine whatever the read came from this animal DNA. What are…
Problem with NextDenovo fungal assembly
Problem with NextDenovo fungal assembly 1 Hi guys, I am new in Genome assembly, I have fungus genome sequencing data from Oxford Nano Tech with 200 X coverage. I used NextDenovo for assembly. I am using my personal system with 32 GB RAM. The parameter file I set is like…
Mapping a small number of contigs to a reference subsequence
Mapping a small number of contigs to a reference subsequence 1 Hello, Is there a method or a tool to align/map a small number of contigs (obtained with Canu) to a subsequence extracted from a reference genome ? For example,in a similar way to reads to reference assembly (using bwa…
minimap2, before or after assembly?
minimap2, before or after assembly? 1 Dear all, I feel confused because I saw someone uses the minimap2 after demultiplexing, but before proceeding with the assembly (CANU) [case 1], and someone using the minimap2/samfile/BFCTools/medaka after assembly (always CANU) [case 2]. In case 1, the reference file used to align against…
Evolution of stickleback spines through independent cis-regulatory changes at HOXDB
Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS PubMed PubMed Central …
Index of /debian-ubuntu/ubuntu/pool/universe/m/minimap2
Name Last modified Size Description Parent Directory – libminimap2-dev_2.24+dfsg-2_amd64.deb 2022-03-25 10:44 132K minimap2_2.17+dfsg-2.debian.tar.xz 2020-01-12 20:18 51K minimap2_2.17+dfsg-2.dsc 2020-01-12 20:18 2.0K minimap2_2.17+dfsg-2_amd64.deb 2020-01-12 20:18 365K minimap2_2.17+dfsg.orig.tar.xz 2019-08-02 02:13 166K minimap2_2.24+dfsg-2.debian.tar.xz 2022-03-25 09:49 11K minimap2_2.24+dfsg-2.dsc 2022-03-25 09:49 2.3K minimap2_2.24+dfsg-2_amd64.deb 2022-03-25 10:44 372K …
Lh3 Minimap2 Issues
Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
In vivo hypermutation and continuous evolution
Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…
Accelerating minimap2 for long-read sequencing applications on modern CPUs ePrints@IISc
Kalikar, S and Jain, C and Vasimuddin, M and Misra, S (2022) Accelerating minimap2 for long-read sequencing applications on modern CPUs. In: Nature Computational Science, 2 (2). pp. 78-83. Full text not available from this repository. Abstract Long-read sequencing is now routinely used at scale for genomics and transcriptomics applications….
Postdoctoral Research Fellow in Bioinformatics/Computational Biology
Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-27118 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with…
Minimap2 detects too many 16S sequences in metagenome
16S is a very conserved sequence, which is why it’s used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which is built around the idea that matching scattered subsequences within a sequence is good enough for identifying matches…
different result using minimap2 and pbmm2
Hi all! I am analysing CSS Pacbio data and each sample came from different run, in particular I have three files for each sample. I tested both pbmm2 and minimap2 to align my long reads, after getting the consensus sequences. This is the command I used to run mnimap2: minimap2…
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…
Mapping back 3 sets of reads/sample with minimap2
I used FaQC to qc my raw fastqs before assembling. That program (and perhaps others) outputs properly paired Forward and Reverse fastqs, as well as an unpaired fastq file for each sample. I used the all 3 for each single sample assembly. Since minimap2 only allows for 2 query files,…
Why did I achieve shorter than initial reads subset after aligned reads extraction.
Why did I achieve shorter than initial reads subset after aligned reads extraction. 1 Hello dear colleages! I have recently faced some problem. I have worked with long WGS reads. Firstly I have filtered the longest subset of reads, and aligned them to the custom sequence with several structural variants…
Debian — File list of package minimap2/bookworm/i386
/usr/bin/minimap2 /usr/share/doc-base/minimap2.minimap2 /usr/share/doc/minimap2/changelog.Debian.gz /usr/share/doc/minimap2/copyright /usr/share/doc/minimap2/minimap2.pdf /usr/share/doc/minimap2/run-unit-test /usr/share/doc/minimap2/test/MT-human.fa.gz /usr/share/doc/minimap2/test/MT-orang.fa.gz /usr/share/doc/minimap2/test/q-inv.fa.gz /usr/share/doc/minimap2/test/q2.fa /usr/share/doc/minimap2/test/t-inv.fa.gz /usr/share/doc/minimap2/test/t2.fa /usr/share/doc/minimap2/test_script /usr/share/man/man1/minimap2.1.gz Read more here: Source link
Minimap2 options for Nanopore cDNA direct seq
Minimap2 options for Nanopore cDNA direct seq 0 Hello, I’m working with ONT RNA seq data and I used the cDNA direct seq to do the seq. I want to look for long deletions in mRNAs that are not spliced, for this, I want to use the splice option of…
Accelerating minimap2 for long-read sequencing applications on modern CPUs
Chaisson, M. J. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 10, 1–16 (2019). Article Google Scholar Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 1–19 (2016). Article Google Scholar Beyter, D. et al. Long-read sequencing of…
bwa-mem2/mm2-fast: Accelerated version of minimap2; up to 1.8x faster
GitHub – bwa-mem2/mm2-fast: Accelerated version of minimap2; up to 1.8x faster This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to…
Accepted minimap2 2.24+dfsg-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 17 Feb 2022 15:33:57 +0100 Source: minimap2 Architecture: source Version: 2.24+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: minimap2 (2.24+dfsg-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: c420faa756a58bcb60927999f3afc21abf91128e 2281 minimap2_2.24+dfsg-1.dsc 8b870031e6b221240cc43b03e117e50a312881ec…
Find Transposon Element insertions using long reads (nanopore), by alignment directly. (minimap2)
find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…
[MonashBioinformaticsPlatform/RSeQC] junction_saturation not suit for bam/sam file generated by minimap or pbmm2
because the CIGAR in bam/sam file generated by minimap2 contain “=” , represent right match with reference, and “X”, represent wrong match with reference. while the bam_cigar.py in ./lib/qcmodule/bam_cigar.py only suit for bam/sam generated such as BWA/bowtie, which CIGAR contain only “M” ,represent mis/match. So i modified the bam_cigar.py 77…
Using Minimap2 with FMLRC2
Using Minimap2 with FMLRC2 1 Hello all, I am using FMLRC2 (github.com/HudsonAlpha/rust-fmlrc) to correct PacBio reads with Illumina reads for hybrid genome assembly. Since FMLRC2 only corrects reads (does not do any assembly) another program is needed. In the paper published on FMLRC minimap (now succeeded by minimap2, github.com/lh3/minimap2) was…
[lh3/minimap2] Memory leak when using Python and threads
The program align.py uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to climb steadily through 40Gb an beyond. This issue was first discovered in bonito and isolated to mappy. The data flow…
Variant calls of published already assembled genomes
Variant calls of published already assembled genomes 0 I have a set of short read sequencing for the 172 KB Epstein-barr virus genome. We successfully called our variants using GATK to a reference genome. A publication linked below from a different population compared variants (also from short read sequencing) to…
Overestimation of number of reads from nanopore data (flagstat)
Same issue as mentioned on the minimap2 tool: github.com/lh3/minimap2/issues/236#issue-361097444 For example nanopore reads aligned to the host transcriptome the flagstat output is: 5953480 + 0 in total (QC-passed reads + QC-failed reads) 2961480 + 0 secondary 22696 + 0 supplementary 0 + 0 duplicates 4195469 + 0 mapped (70.47% :…
Samtools flagstat
Samtools flagstat 1 I aligned my ONT sequencing run with minimap2, subsequently I filtered the file using samtools view -b -F 256 aln_transcriptome_sorted_6.bam -o filtered_aln_transcriptome_6.bam to end up with primary alignments only. When I run samtools flagstat on the filtered file I get the following output: 3502608 + 0 in…
minimap2 – Github Help
38 9 7 minimap2,SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by…
About QUAST
About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…
A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…
sniffles failed detect SV on minimap2 aligments
When I use ngmlr the sniffles worked. The coverage it more than 90% The code I sent on the github is exactly what it generated, I don’t think there any error Xu Zhang PhD Postdoctoral Associate, Department of Microbiology and Immunology Weill Cornell Medicine 1300 York Avenue, Box 62 New…
#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression
#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression – Debian Bug report logs Reported by: Paul Gevers <elbrus@debian.org> Date: Tue, 14 Dec 2021 20:03:02 UTC Severity: serious Tags: bookworm, sid Found in version minimap2/2.17+dfsg-12 Fixed in version minimap2/2.22+dfsg-3 Done: Paul Gevers <elbrus@debian.org> Reply or subscribe…
Towards the biogeography of prokaryotic genes
1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed Google Scholar 2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS PubMed PubMed Central Google Scholar 3. Mohammad,…
Bug#1001716: src:minimap2: fails to migrate to testing for too long: autopkgtest regression
Source: minimap2 Version: 2.17+dfsg-12 Severity: serious Control: close -1 2.22+dfsg-3 Tags: sid bookworm User: release.debian….@packages.debian.org Usertags: out-of-sync Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 60 days as having a Release Critical bug in testing [1]. Your package src:minimap2 has been…
Mapping multiples
Mapping multiples 1 Hi, I am coming to you for help. I am doing a mapping on short and long read files with BWA and MINIMAP2 My problem is that, I want to make an if loop that would allow me to choose either BWA if I work with short…
The Biostar Herald for Tuesday, September 14, 2021
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
How to plot the gap distribution of contigs wrt to reference genome
How to plot the gap distribution of contigs wrt to reference genome 0 I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of…
Pacific Biosciences hiring Bioinformatics Software Engineer in United States
PacBio’s Application Software Group focuses on building solid, strategic value around our core data type – highly accurate, long read sequencing – by producing innovative software that unlocks genomics in ways never seen before. We’re growing an interdisciplinary team of bioinformatic experts to tackle some of the most interesting problems…
The Biostar Herald for Friday, September 03, 2021
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from zx8754, Istvan Albert, and was edited by…
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance
1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS PubMed PubMed Central Google Scholar 2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS PubMed Article Google…
unable to find chromosome in SAM header
featureCounts: unable to find chromosome in SAM header 0 I am using featureCounts to try and create a count table for some RNA-Seq data I collected using an Oxford Nanopore platform. I have .sam files aligned with minimap2, and am running the following command to try to get a count…