SeqFu is a tool to help you manage your sequence files. It is a command-line tool that can be used to filter, transform, and manipulate sequence files in various formats. SeqFu is designed to be fast and efficient, and it is written in Rust.

Some functions

SeqFu has a set of subtools like:

• seqfu stats to get statistics of FASTA and FASTQ files, including N50 (supports gzipped files)
• seqfu head and seqfu tail will print the first or last sequences. With options to print one every N and more.
• seqfu cat, to reshape FASTA/FASTQ files, adding prefixes or suffixes to the names, removing comments, etc.
• seqfu interleave and seqfu deinterleave

and many other tools!

Installation

You can install if from conda

conda install -y -c conda-forge -c bioconda seqfu

Alternatively, you can download pre-compiled binaries and put them on your PATH. Note that in the EBAME VM you have SeqFu in ~/bin/.

Anvi’o special

seqfu cat --anvio ASSEMBLY > RENAMED_ASSEMBLY.fa

will substitute anvi-script-reformat-fasta. It’s faster, and being SeqFu easy to install, you can embed this step in your pipeline to get Anvi’o ready contigs.

Visual commands

• seqfu view

You can have a quick look at FASTQ files (to check for quality and primers/adapters):

seqfu cat FASTQ_FILE | less -SR

• fu-msa

To check multiple alignment files from the command line:

fu-msa MSA.fa