fq2dna (FASTQ files to de novo assembly) is a command line tool to ease the de novo assembly oƒ archaea, bacteria or virus genomes ƒrom raw high-throughput sequencing (HTS) paired-end (PE) reads.
Every data pre- and post-processing step is managed by fq2dna (e.g. HTS read ƒiltering and enhancing, well-tuned de novo assemblies, scaffold sequence accuracy assessment). The main purpose of fq2dna is to eƒƒiciently use different methods, programs and tools to quickly inƒer accurate genome assemblies (e.g. from 5 to 15 minutes to deal with a bacteria HTS sample using 12 threads). This mini-workƒlow can thereƒore be very useƒul to deal with large batches of whole-genome shotgun sequencing data.
fq2dna is ƒreely available at gitlab.pasteur.fr/GIPhy/fq2dna. It runs on UNIX, Linux and most OS X operating systems.