sickle - A windowed adaptive trimming tool for FASTQ files using quality
Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end. Incorrectly called bases here negatively impact assembles, mapping, and downstream bioinformatics analyses.
Sickle is a tool that uses sliding windows to determine when quality is sufficiently low to trim the 3'-end of reads.
Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source.
Sickle also requires Zlib, which can be obtained at http://www.zlib.net/.
Building and Installing Sickle
To build Sickle, enter:
Then, copy or move "sickle" to a directory in your $PATH.
Sickle has two modes to work with both paired-end and single-end
sickle pe and