ƒqCleanER (ƒastq Cleaning and Enhancing Routine) is a command line tool to ease the diƒƒerent standard preprocessing steps oƒ short high-throughput sequencing (HTS) reads.
Eight standard HTS read processing steps can be carried out using ƒqCleanER :
❶ contaminating HTS read removal,
❷ sequencing error correction,
❸ HTS read deduplication,
❹ low-coverage HTS read removal,
❺ digital normalization,
❻ paired-ends HTS read merging,
❼ high-coverage HTS read reduction,
❽ HTS read trimming and clipping.
All these steps may be performed in any order, on up to three paired- and/or single-end FASTQ ƒiles (compressed or not).
ƒqCleanER is ƒreely available at gitlab.pasteur.fr/GIPhy/fqCleanER. It runs on UNIX, Linux and most OS X operating systems.