cutadapt pipeline

cutadapt specifications


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



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Publication for cutadapt

cutadapt IN pipelines

PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17

[…] prep library kit (kapa biosystems) and sequenced on an illumina miseq platform using a 250-bp paired-end format, resulting in a total of 5,320,190 reads. the raw sequences were preprocessed using cutadapt version 1.14 to trim adaptors (10) and using prinseq version 0.20.4 to perform quality filtering (11). initial genome assembly was performed with the spades version 3.10.0 genome assembler […]

PMCID: 5759179
PMID: 29354114
DOI: 10.3389/fmicb.2017.02630

[…] concerned the accessions ranging from srr1542919 to srr1542936 (table 1). reads in the associated measurements were first cleaned by removing adapters, low quality regions, or complete reads using cutadapt (martin, 2011) and sickle (joshi and fass, 2011). the quality score cutoff was set to 30 in respect to quality trimming, and the minimum length of read threshold was set to 30. following […]

PMCID: 5761188
PMID: 29316957
DOI: 10.1186/s13058-017-0929-z

[…] ( raw reads (fastq files) were first quality-checked using fastqc (v0.11.2; and trimmed using cutadapt (1.7.1) [19] to ensure high read quality. filtered reads were then aligned to the human reference genome (grch37/hg19) using the burrows-wheeler aligner tool [20], with base quality score […]

PMCID: 5794942
PMID: 29437095
DOI: 10.1128/genomeA.01520-17

[…] colony in a yeast extract-peptone-dextrose (yepd) medium at 20°c. the sequencing of a truseq dna library (250-nucleotide [nt] reads) generated 15,314,404 reads. sequencing primers were removed using cutadapt (5) and low-quality read regions were trimmed using sickle ( illumina reads were de novo assembled using spades 3.7.1 (6). contigs shorter than 200 bp […]

PMCID: 5797788
PMID: 29445324
DOI: 10.3389/fnmol.2017.00435

[…] whole-genome sequencing of the sample. the library was sequenced on the hiseq 2500 sequencer (illumina), yielding 150-bp paired-end reads. the library adapter sequences at 3′ ends were removed with cutadapt 1.7.1 (martin, 2011) and low-quality bases (q-score < 16) at both ends were then trimmed using a custom script. pairs containing a read that was shorter than 36 nt were eliminated. […]

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