Results for "Reads"


  • 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

    580 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

    572 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

    538 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

    546 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

    546 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

    483 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

    539 days ago

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

    Tags: Extract, Chromosome, Number, Reads

    532 days ago

  • Reads QC #Quality #Reads #NGS

    Tags: Quality, Reads, NGS

    492 days ago

  • How MIRA follows for the ref based assembly?

    MIRA follows for the ref based assembly (like mapping the reads on the reference with xxx, etc.) and if its possible to have a figure with the workflow.

    Tags: Mira, Assembly, Flow, Workflow, Reads

    524 days ago