Sickle

Description

sickle website

Sickle is a tool that uses sliding sequence windows along with quality and length thresholds to determine for intelligent 3'/5'-end trimming of short reads. 5'-end trimming can be disabled. Sickle also has an option to discard reads with any Ns in them. Sickle supports three types of quality values: Illumina, Solexa, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sanger encoded. Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it with simply a "+". This is the default format for CASAVA >= 1.8.

Environment Modules

Run module spider sickle to find out what environment modules are available for this application.

Environment Variables

• HPC_SICKLE_DIR - installation directory
• HPC_SICKLE_BIN - executable directory

Categories

biology, ngs