Reformat pipeline

Reformat specifications


Unique identifier OMICS_17797
Name Reformat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output format FASTA, FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Brian Bushnell <>

Additional information

Reformat IN pipelines

PMCID: 5804319
PMID: 29423345
DOI: 10.7717/peerj.4320

[…] the noise filtering parameters described by minoche, dohm & himmelbauer (2011). after simplifying the header lines of 31 fasta files for prochlorococcus isolate genomes using the anvi’o script ‘reformat-fasta’, we concatenated all fasta files into a single file, and used bowtie2 (langmead & salzberg, 2012) with default parameters and the additional ‘--no-unal’ flag to recruit […]

PMCID: 5162099
PMID: 27986076
DOI: 10.1186/s12864-016-3377-8

[…] for variant discovery. then, snp and indels based on the mapped reads were called using samtools mpileup v0.1.7a ( [55] and bcftools. custom perl scripts were used to reformat the original output and filter the snps based on coverage and probability. another perl script was used to identify in which gene each snp was found and where it was located relative […]

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