v2.0.0-alpha · FASTA / FASTQ toolkit

Inspect, filter and reshape sequence files from the command line.

SeqFu is a fast, general-purpose toolkit for FASTA and FASTQ files, gzipped or not. Core programs run as seqfu <command>;
Dev version, the stable version is here.

Stable version (1.x) Get started Browse commands

# Install the stable release from Bioconda$ conda install -c conda-forge -c bioconda "seqfu>=1.30"

# Download and run the install script$ curl -fsSL https://telatin.github.io/seqfu2/install.sh | sh

# Clone the repository and build from source.# Requires Nim 2.2 or newer.$ git clone https://github.com/telatin/seqfu2 && cd seqfu2 && make

Bioconda currently installs the stable SeqFu 1.x release, not the development version documented here. See the stable version documentation.

Examples

# Summary statistics (N50, lengths…) as a readable table

$ seqfu stats -n *.fq.gz

# Print the first 10 sequences of a file

$ seqfu head -n 10 interleaved.fq.gz

# Keep sequences containing an oligo (IUPAC, both strands)

$ seqfu grep -o AGTGGCGGACGGGTGA 16S_coli.fa

# Count reads, checking that paired files match

$ seqfu count illumina_1.fq.gz illumina_2.fq.gz

Core tools35 commands seqfu <command> [options] FILE... Subcommands of the main seqfu binary, with a stable, tested command-line interface. Utilities14 tools fu-<tool> [options] FILE... Standalone fu-* programs shipped with SeqFu, including compatibility wrappers.

Find a tool by task

Commands grouped by what they do, across both core tools and utilities.

Inspection5 head · less · msa · tail Statistics & QC8 amplicheck · bases · check · count Filtering & extraction12 adapters · by-comment · by-id · by-seq Transformation9 cat · homocomp · rc · rotate Pairing & lanes4 deinterleave · interleave · lanes · merge Metadata & tables4 metadata · tabcheck · tabulate · fu-tabcheck Specialised analysis5 orf · fu-16Sregion · fu-nanotags · fu-orf

Recipes

Inspect a new sequencing run check · count · stats Prepare and validate a sample sheet metadata · tabcheck · check Merge lanes per sample lanes · count Dereplicate amplicon reads derep · sort · stats Extract reads by a list of IDs list · by-id · subtract Filter and rename an assembly stats · fu-cov · cat

All recipes →

Cite SeqFu

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8(5), 59.

doi:10.3390/bioengineering8050059