Trim Galore! protocols

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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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Additional information


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

Publication for Trim Galore!

Trim Galore! in pipelines

 (175)
2018
PMCID: 5754475
PMID: 29301895
DOI: 10.1128/genomeA.00839-17

[…] (). purified phage dna was sequenced at molecular research lp (shallowater, tx) using an illumina miseq (2 × 300 bp) platform. the raw reads were checked for quality and adapter contamination using trim galore () and then assembled into contigs using a spades genome assembler (). dna ends were conformed via pcr. genes were predicted using genemark () and were manually annotated using the ncbi […]

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 ). 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) [] were aligned to the mm9 genome assembly using bowtie2 v2.1.0 [] and uniquely aligned reads […]

2018
PMCID: 5788746
PMID: 29337073
DOI: 10.1016/j.cub.2017.11.060

[…] strain were sequenced across a single lane of an illumina hiseq2500 using a 250 bp paired-end read metric. fastqc was used to check the quality of the raw reads obtained [] and reads trimmed using trim galore []. in initial attempts to estimate gene copy number the reads of each strain were mapped to the reference genome (sequenced from an inbred line derived from a strain collected […]

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 […]


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Trim Galore! in publications

 (482)
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] using an illumina hiseq 2500 platform (2 × 125-bp read length) at the donnelly sequencing center, university of toronto (canada)., 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 […]

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

[…] 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. […]

PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] control measures before sequencing on the illumina miseq platform., 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 […]

PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913

[…] of southern california., 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 […]

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

[…] (bd biosciences) and compensation was performed with the in-build compensation tool (bd facsdiva software) using single stained samples., 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 […]


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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 :)
yinhz0626's avatar image

yinhz0626

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very good software