RabemaBuildGoldStandard

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.

Web Documentation for RabemaBuildGoldStandard

Options

version-check
Turn this option off to disable version update notifications of the application.
verbose
Enable verbose output.
very-verbose
Enable even more verbose output.
oracle-mode
Enable oracle mode. This is used for simulated data when the input SAM/BAM file gives exactly one position that is considered as the true sample position.
match-N
When set, N matches all characters without penalty.
distance-metric
Set distance metric. Valid values: hamming, edit. Default: edit.
max-error
Maximal error rate to build gold standard for in percent. This parameter is an integer and relative to the read length. In case of oracle mode, the error rate for the read at the sampling position is used and RATE is used as a cutoff threshold.

Input Ports

Icon
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]
Icon
Path to load the "perfect" SAM/BAM file from. [bam,sam,sam.bgzf,sam.gz,opt.]

Output Ports

Icon
Path to write the resulting GSI file to. [gsi,gsi.gz]

Popular Predecessors

Popular Successors

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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

Further Links

Developers

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