Tag: minimap2

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….

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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…

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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…

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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…

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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…

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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,…

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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…

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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…

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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…

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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…

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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…

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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,…

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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…

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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….

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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…

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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…

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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….

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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…

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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…

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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…

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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…

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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 …

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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…

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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…

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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…

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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,…

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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,…

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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?…

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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 …

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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:…

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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…

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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,…

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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,…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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 …

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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  …

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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…

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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….

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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…

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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….

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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…

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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…

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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…

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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…

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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,…

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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…

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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

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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…

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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…

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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…

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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…

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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&#13; $ 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…

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[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…

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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…

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[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…

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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…

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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% :…

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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…

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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…

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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…

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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…

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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…

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#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…

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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,…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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hisat2 compatibility for long read

hisat2 compatibility for long read 0 Hi, I am trying to align PacBio transcriptome reads against the genome to count the gene number. For pair end read i used the following workflow: # convert gff to gtf /home/software/cufflinks-2.2.1/gffread xxx.gff -T -o xxx.gtf # build index /home/software/hisat2-2.2.1/hisat2_extract_exons.py xxx.gtf > xxx.exon /home/software/hisat2-2.2.1/hisat2_extract_splice_sites.py…

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De novo genome assembly

Forum:De novo genome assembly 0 Howdy, I have recently been tasked as the ‘bioinformatics guy” in my lab and am having trouble with a de novo genome assembly of Mother of a Thousand. I am working with Nanopore reads and have ran my reads through CANU. I have all of…

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