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cutadapt specifications


Unique identifier OMICS_01086
Name cutadapt
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Publication for cutadapt

cutadapt citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] d line programs for data analysis were run on the bioinformatics cluster of CGR (University of Liverpool) in a Debian 5 or 7 environment.Raw fastq files were trimmed to remove Illumina adapters using Cutadapt version 1.2.1 with option -O 3 () and Sickle version 1.200 with a minimum quality score of 20 (). Further quality control was performed with Prinseq-lite () with the following parameters: min […]


“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”

BMC Infect Dis
PMCID: 5952419
PMID: 29764370
DOI: 10.1186/s12879-018-3127-4
call_split See protocol

[…] umina Hiseq2500. On average 49–50 million basepair (bp) reads were produced per sample. Quality check of reads was performed with the software FastQC. Low quality reads and adapters were trimmed with Cutadapt []. Trimmed reads were mapped to the human genome GRCh38/hg19 with STAR [], and the expression level for each gene was counted with HTSeq [] according to gene annotations from Ensembl. The Bi […]


High‐throughput discovery of functional disordered regions: investigation of transactivation domains

Mol Syst Biol
PMCID: 5949888
PMID: 29759983
DOI: 10.15252/msb.20188190

[…] t tolerating more than 1 expected error across the read after taking the quality scores per base into account. Next, the replicate barcode sequences (present in the design library) were removed using cutadapt (Martin, ), recording the replicate barcode identifier in the fasta header. Barcodes were designed to have a length of eight nucleotides and to have a Levenshtein distance of at least four, i […]


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

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

[…] ized genome sequences generated (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 […]


Small RNA profiling of low biomass samples: identification and removal of contaminants

BMC Biol
PMCID: 5952572
PMID: 29759067
DOI: 10.1186/s12915-018-0522-7

[…] For the initial analysis of plasma-derived sRNA sequencing data, FastQC [] was used to determine over-represented primer and adapter sequences, which were subsequently removed using cutadapt []. This step was repeated recursively until no over-represented primer or adapter sequences were detected. 5’-Ns were removed using fastx_clipper of the FASTX-toolkit. Trimmed reads were qua […]


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9
call_split See protocol

[…] Reads were mapped to the human reference genome hg19 with the STAR (version 2.5.0b) aligner. Low-quality reads (mapping quality <20) as well as known adapter contaminations were filtered out using Cutadapt (version 1.10.0). Read counting was performed using Bioconductor packages Rsubread and differential expression analysis with edgeR,. The conditions were contrasted against the growing samples […]


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cutadapt institution(s)
Department of Computer Science, TU Dortmund, Germany
cutadapt funding source(s)
Supported by Mercator Research Center Ruhr, Germany, grant Pr-2010-0016.

cutadapt review

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Anonymous user #60's avatar image No country

Anonymous user #60

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Very useful to remove adapters in read 3'end, allowing for mismatches due to sequencing errors. Con: python dependencies