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Sickle

Allows windowed adaptive trimming. Sickle determines when quality is sufficiently low to trim the 3'-end of reads and also when the quality is sufficiently high enough to trim the 5'-end of reads, using sliding windows along with quality and length thresholds. The software supports three types of quality values: Illumina, Solexa, and Sanger.

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Sickle classification

Sickle specifications

Unique identifier:
OMICS_01077
Interface:
Command line interface
Input data:
Two paired-end file or a single combined file of reads where you have already interleaved the reads from the sequencer.
Output data:
Two trimmed paired-end files as well as a "singles" file or reads that passed filter in either the forward or reverse direction, and one optional interleaved output file where any reads that did not pass filter will be output as a FastQ record with a single "N".
Programming languages:
C
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://codeload.github.com/najoshi/sickle/tar.gz/v1.33
Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTQ
Operating system:
Unix/Linux
License:
MIT License
Version:
1.33
Requirements:
C compiler, Zlib.
Maintained:
Yes

Sickle distribution

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Sickle support

Documentation

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.