[ Bron: trim-galore ]
Pakket: trim-galore (0.6.10-1)
Verwijzigingen voor trim-galore
Debian bronnen:
Het bronpakket trim-galore downloaden:
Beheerders:
Externe bronnen:
- Homepage [www.bioinformatics.babraham.ac.uk]
Vergelijkbare pakketten:
automate quality and adapter trimming for DNA sequencing
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
* For adapter trimming, Trim Galore! uses the first 13 bp of Illumina
standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends
of paired-end libraries), but accepts other adapter sequence, too
* For MspI-digested RRBS libraries, Trim Galore! performs quality and
adapter trimming in two subsequent steps. This allows it to remove
2 additional bases that contain a cytosine which was artificially
introduced in the end-repair step during the library preparation
* For any kind of FastQ file other than MspI-digested RRBS, Trim
Galore! can perform single-pass adapter- and quality trimming
* The Phred quality of basecalls and the stringency for adapter removal
can be specified individually
* Trim Galore! can remove sequences if they become too short during
the trimming process. For paired-end files Trim Galore! removes entire
sequence pairs if one (or both) of the two reads became shorter than
the set length cutoff. Reads of a read-pair that are longer than a
given threshold but for which the partner read has become too short
can optionally be written out to single-end files. This ensures that
the information of a read pair is not lost entirely if only one read
is of good quality
* Trim Galore! can trim paired-end files by 1 additional bp from the 3'
end of all reads to avoid problems with invalid alignments with Bowtie 1
* Trim Galore! accepts and produces standard or gzip compressed FastQ files
* FastQC can optionally be run on the resulting output files once
trimming has completed