[ Источник: trim-galore ]
Пакет: trim-galore (0.6.6-1)
Ссылки для trim-galore
Ресурсы Debian:
- Сообщения об ошибках
- Developer Information
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Исходный код trim-galore:
Сопровождающие:
Внешние ресурсы:
- Сайт [www.bioinformatics.babraham.ac.uk]
Подобные пакеты:
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
Другие пакеты, относящиеся к trim-galore
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- dep: cutadapt
- Clean biological sequences from high-throughput sequencing reads
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- dep: perl
- практический язык Ларри Уолла для извлечения данных и составления отчётов
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- rec: fastqc
- quality control for high throughput sequence data
Загрузка trim-galore
Архитектура | Размер пакета | В установленном виде | Файлы |
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all | 17 401,0 Кб | 17 520,0 Кб | [список файлов] |