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.
Options
Input Ports
- 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]
- Pre-correction SAM file. [sam,bam]
- Post-correction SAM file. [sam,opt.]
- Post-correction FASTQ or FASTA file. [fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz,opt.]
Views
- ComputeGain Std Output
- The text sent to standard out during the execution of ComputeGain.
- ComputeGain Error Output
- The text sent to standard error during the execution of ComputeGain. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
Workflows
- No workflows found
Links
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Developers
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