SeqFu

See the repository | releases

A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS.

• A compiled program delivering high performance analyses
• Supports FASTA/FASTQ files, also Gzip compressed
• A growing collection of handy utilities, also for quick inspection of the datasets
• UNIX like commands but specific for sequences like seqfu cat, seqfu head, seqfu tail, seqfu grep
• Terminal friendly reports from seqfu stats or seqfu count…

Can be easily installed via conda:

conda install -c conda-forge -c bioconda "seqfu>1.0"

Citation

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059

Contents

• Installation
• Overview
• Short guide
• About SeqFu
• Core Tools
  • seqfu bases
  • seqfu cat
  • seqfu check
  • seqfu count
  • seqfu deinterleave
  • seqfu derep
  • seqfu grep
  • seqfu head
  • seqfu interleave
  • seqfu lanes
  • seqfu list
  • seqfu merge
  • seqfu metadata
  • seqfu qual
  • seqfu rc
  • seqfu rotate
  • seqfu sort
  • seqfu stats
  • seqfu tabulate
  • seqfu tail
  • seqfu view
• Utilities
  • fu-16Sregion
  • fu-cov
  • fu-homocom
  • fu-index
  • fu-msa
  • fu-multirelabel
  • fu-nanotags
  • fu-orf
  • fu-primers
  • fu-shred
  • fu-sw
  • fu-tabcheck
  • fu-virfilter
• Helper utilities
  • fu-pecheck
  • fu-split
• Releases
  • Release history