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QAtoFasta

Overview

QAtoFasta transforms QAFastq format into standard FASTA format files, which is widely used in 3rd party software.

Two different quality values are suggested for masking low quality regions in the FASTA files.

1. Q >= 0. This will maintain all consensus calls from the assembly. This transform is suggested for gene predictions and similarity searches.
2. Q >= 10. This will mask all the low quality bases. This transform is suggested for SNP calling or highly accurate MLST typing.

The QAssembly pipeline runs QAtoFasta in order to process the assemblies generated by QAssembly with Q >= 0, prior to running the QA evaluation pipeline. (However, the QA evaluation pipeline processes the sequence to obtain the masked sequence that is made available to download in FASTA format itself, without running the code in QAFasta.)

The current version of QAtoFasta is 1.0.

Inputs/Outputs

Parameters

{
    "params": {
        "low_qual": 10
    },
    "inputs": {
        "fastq": "SAL_AA0001AA_AS.scaffold.fastq"
    },
    "outputs": {
        "fasta": "SAL_AA0001AA_AS.scaffold.fasta"
    }
}

Outputs

{
    "outputs": {
        "fasta": ["SAL_AA0001AA_AS.scaffold.fasta", "/path/to/folder/SAL_AA0001AA_AS.scaffold.fasta" ]
    }
}