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This program allows one to build a RABEMA gold standard. The input is a reference FASTA file and a perfect SAM/BAM map (e.g. created using RazerS 3 in full-sensitivity mode).
The input SAM/BAM file must be sorted by coordinate. The program will create a FASTA index file REF.fa.fai for fast random access to the reference.
Options
Input Ports
- Path to load reference FASTA from. [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]
- Path to load the "perfect" SAM/BAM file from. [bam,sam,sam.bgzf,sam.gz,opt.]
Views
- RabemaBuildGoldStandard Std Output
- The text sent to standard out during the execution of RabemaBuildGoldStandard.
- RabemaBuildGoldStandard Error Output
- The text sent to standard error during the execution of RabemaBuildGoldStandard. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
Workflows
Links
- No links available
Developers
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