ComputeGain

Manipulator

This program computes the read correction tool metric GAIN. It takes a genome FASTA file and two SAM file with read alignments before and after correction. It then computes various statistics and computes the GAIN, based on the edit or Hamming distance for reach read before and after correction.

Web Documentation for ComputeGain

Input Ports

  1. Type: URI Object
    Genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
  2. Type: URI Object
    Pre-correction SAM file. [sam,bam]
  3. Type: URI Object
    Post-correction SAM file. [sam,opt.]
  4. Type: URI Object
    Post-correction FASTQ or FASTA file. [fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz,opt.]

Output Ports

  1. Type: URI Object
    Write log about introduced/removed errors to this file. []

Extension

This node is part of the extension

SeqAn

v2.4.0

Short Link

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