Trim Galore! statistics

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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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Versioning


No version available

Maintainer


Additional information


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

Publication for Trim Galore!

Trim Galore! citations

 (476)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] Raw FASTQ sequence reads were subjected to adapter trimming using Trim Galore v0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and were quality checked using FASTQC v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Genomes w […]

library_books

Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

2018
Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] (as described earlier).Allele-specific alignment of single cell mRNA libraries: FASTQ files of the sequenced transcripts were run through FastQC tool (version 0.10.1), Cutadapt tool (version 1.2) and Trim Galore (version 0.4.1) to remove transposase sequence remainders (CTGTCTCTTATACAC). Files then were aligned against the generated transcriptome reference using BWA 6.2 with default parameters. We […]

call_split

Complex signatures of genomic variation of two non model marine species in a homogeneous environment

2018
BMC Genomics
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y
call_split See protocol

[…] The quality of raw reads from the MiSeq facility was first assessed with the FASTQC toolkit []. The reads were then trimmed with Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), trimming adapter and overrepresented sequences, as well as sections with bases having a Phred quality score lower than 2 […]

call_split

Optimizing exosomal RNA isolation for RNA Seq analyses of archival sera specimens

2018
PLoS One
PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913
call_split See protocol

[…] Raw data were downloaded as FASTQ files and QC performed using MultiQC []. Around 10 million reads were generated for each sample. The raw data was pre-processed using Trimgalore version 0.4.2 [] to remove Illumina adapters and reads shorter than 20 bp. Trimmed reads were aligned to version hg38 of the human genome reference sequence using STAR []. Mapped reads were […]

library_books

Time resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

2018
BMC Biol
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] FASTQ files were adapter- and quality-trimmed using Trim Galore!, and aligned with TopHat2 using hg19 genome index and GENCODE v19 transcriptome model. Alignment metrics and statistics were extracted from the BAM files using Picard tools. Reads were su […]

library_books

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

2018
BMC Genomics
PMCID: 5922311
PMID: 29695257
DOI: 10.1186/s12864-018-4675-0

[…] RNA-seq was performed as previously described []. Briefly, Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and Trimmomatic [] were used to remove adaptor sequences and low-quality base calls from the sequencing reads. Firstly, Tri […]

Citations

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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 :)
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Anonymous user #5515

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Desktop
very good software