ComputeGain

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 [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]
   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 [sam,bam]
   Pre-correction SAM file. [sam,bam]
3. Type: URI Object
   post-sam [sam]
   Post-correction SAM file. [sam,opt.]
4. Type: URI Object
   post [fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz]
   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
   correction-log []
   Write log about introduced/removed errors to this file. []