Trim Galore! protocols

Trim Galore! specifications

Information


Unique identifier OMICS_01096
Name Trim Galore!
Alternative names Trim Galore, TrimGalore, Trim_Galore!
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.5
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Felix Krueger <>

Additional information


https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md

Publication for Trim Galore!

Trim Galore! IN pipelines

 (84)
2018
PMCID: 5760651
PMID: 29317678
DOI: 10.1038/s41467-017-02618-6

[…] ipswich, ma, usa). libraries were sequenced on the illumina hiseq 2500 instruments, with 30 million 2 × 50 bp paired reads., for chip-seq analysis, reads were quality and adapter trimmed using ‘trim_galore’ before aligning to human genome assembly hg19 with bwa mem using the default parameters. aligned reads with the same start position and orientation were collapsed to a single read […]

2018
PMCID: 5775534
PMID: 29351814
DOI: 10.1186/s13059-017-1376-y

[…] adaptors and adds sample barcodes, allowing for multiplexing (see primers in additional file 3). paired-end sequencing of pooled samples was done using an illumina miseq., reads were trimmed using trim_galore! v0.3.3 with default parameters. external chip-seq data for h4r3me2s (geo accession gse37604) [36] were aligned to the mm9 genome assembly using bowtie2 v2.1.0 [44] and uniquely aligned […]

2018
PMCID: 5788912
PMID: 29422865
DOI: 10.3389/fphys.2018.00008

[…] raw reads passed quality filtering. briefly, the quality of the raw reads was assessed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and low qualities were filtered out by trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). tiltered reads were mapped to reference genome using tophat; gene assembly and differential gene expressions […]

2018
PMCID: 5788912
PMID: 29422865
DOI: 10.3389/fphys.2018.00008

[…] raw reads was assessed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and low qualities were filtered out by trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). tiltered reads were mapped to reference genome using tophat; gene assembly and differential gene expressions were determined using cufflinks (trapnell et al., 2012)., the gene […]

2018
PMCID: 5790871
PMID: 29404424
DOI: 10.1128/mSystems.00108-17

[…] loci in clonal bacterial populations., we downloaded sequencing read data from two large surveys of drug-resistant m. tuberculosis in russia (5) and south africa (6). we used fastqc (55) and trimgalore! (56) for quality assessment and adaptor trimming of the reads. trimmed reads were mapped to m. tuberculosis h37rv (accession no. nc_000962.3) using bwa-mem v 0.7.12 (57). we used samtools […]

Trim Galore! institution(s)
TNLIST/Department of Automation, Tsinghua University, Beijing, China

Trim Galore! reviews

 (2)
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David Twesigomwe

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Trim Galore! is a very efficient quality and adapter trimmer for single-end as well as paired-end reads. It has various options that make it user-friendly including;
- allowing for both automatic detection of adapter sequences to be trimmed as well as user-defined adapter sequences
- allowing for user-defined stringency of adapter removal and Phred quality of base calls
- using two-step adapter and quality trimming for MspI-digested RRBS libraries thus removing biased methylation positions
- allowing for single-pass adapter and quality trimming for FASTQ files other than MspI-digested RRBS
- optional removal of bp from the 3' end of a read to remove some unwanted bias that is not directly related to adapter sequence or base call quality
- removing reads that become shorter than a set cutoff during the trimming process while providing an option to write out a good-length read to a single-end file in case the partner read is shorter than the set cutoff.
- allowing for trimming paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments especially if one is using Bowtie 1
For the above functionalities, I give Trim Galore! a 5-star! Credit to the developers at Babraham Institute :)
yinhz0626's avatar image

yinhz0626

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very good software