Results for "Reads"

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  • mrFAST: Micro Read Fast Alignment Search Tool

    mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...

    Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference

    426 days ago

  • segemehl

    segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation conta...

    Tags: Bioinformatics, FASTQ, Reads, Map, Mapping, Segemehl, NGS

    412 days ago

  • cutadapt

    Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longe...

    Tags: Bioinformatics, Cutadapt, NGS, Reads, Fastq, Sequencing

    409 days ago

  • Stampy

    Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation ...

    Tags: Bioinformatics, NGS, Stampy, Reads, Mapping, Map

    401 days ago

  • #Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

    Tags: Extract, Reads, BAM, region, samtools

    367 days ago

  • LoRMA

    LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016. ...

    Tags: Bioinformatics, LoRMA, Tool, Correcting, Errors, Reads, Sequencing

    375 days ago

  • CovCal

    Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration and genome size, then select what you want to calculate. Written by Stephen Turner, based on the Lander-Wate...

    Tags: Bioinformatics, covcal, Tool, Coverage, Reads, Sequencing

    375 days ago

  • How to extract 50% of the reads?

    I would like to extract a subset of PE reads (50%) and store them in seperate files. It should be in both way "split by middle" or "random". Is there any way to achieve it?

    Tags: Reads, NGS, PE, Extract

    312 days ago

  • WgSim

    Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...

    Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation

    368 days ago

  • #Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

    Tags: Extract, Chromosome, Number, Reads

    361 days ago