mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-06 08:26:50 +01:00
38 lines
1.6 KiB
Text
38 lines
1.6 KiB
Text
Trimmomatic: A flexible read trimming tool for Illumina NGS data
|
|
|
|
Trimmomatic performs a variety of useful trimming tasks for illumina
|
|
paired-end and single ended data.The selection of trimming steps and
|
|
their associated parameters are supplied on the command line.
|
|
|
|
The current trimming steps are:
|
|
|
|
- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
|
|
the read.
|
|
- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
|
|
average quality within the window falls below a threshold.
|
|
- LEADING: Cut bases off the start of a read, if below a threshold
|
|
quality
|
|
- TRAILING: Cut bases off the end of a read, if below a threshold
|
|
quality
|
|
- CROP: Cut the read to a specified length
|
|
- HEADCROP: Cut the specified number of bases from the start of the
|
|
read
|
|
- MINLEN: Drop the read if it is below a specified length
|
|
- TOPHRED33: Convert quality scores to Phred-33
|
|
- TOPHRED64: Convert quality scores to Phred-64
|
|
|
|
It works with FASTQ (using phred + 33 or phred + 64 quality scores,
|
|
depending on the Illumina pipeline used), either uncompressed or
|
|
gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
|
|
extension.
|
|
|
|
For single-ended data, one input and one output file are specified,
|
|
plus the processing steps. For paired-end data, two input files are
|
|
specified, and 4 output files, 2 for the 'paired' output where both
|
|
reads survived the processing, and 2 for corresponding 'unpaired'
|
|
output where a read survived, but the partner read did not.
|
|
|
|
Citations
|
|
Bolger, A. M., Lohse, M., & Usadel, B. (2014).
|
|
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
|
|
Bioinformatics, btu170.
|