Citing
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
Why
There are several tools for the analysis of FASTQ/FASTA files. My personal choice has been (and is) SeqKit, a general purpose toolkit.
As many other bioinformaticians, I found myself coding small ad hoc scripts, for example:
- A tool to extract the index from Illumina FASTQ files (taking the most common occurrence from the first 1000 reads)
- A tool to extract contigs using a list from a predictor
- Scripts to interleave/deinterleave FASTQ files
The problem was distributing a very small script to users lacking the library I was using (like the excellent pyfastx or our FASTX::Reader).
The possibility to distribute self-contained binaries was an option that was both boosting the performance of the program, and solving the dependency hell for minor applications.
This led to the start of the project.
How
SeqFu is written in Nim, which compiles to fast, dependency-free
binaries. FASTA/FASTQ parsing is provided by readfx,
which wraps Heng Li’s kseq.h (lh3/biofast); earlier versions
used klib.nim and nimreadfq.
About the name
The name of the program was modeled after “ScriptFu”, a set of macros built in the image manipulation GIMP.