Btrim pipeline

Btrim specifications

Information


Unique identifier OMICS_01083
Name Btrim
Alternative name Btrim64
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Btrim

Btrim IN pipelines

 (15)
2018
PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] 41] and 100-bp reads were obtained by using an illumina hiseq2000 sequencer (illumina, san diego, ca, usa). low-quality nucleotides (<q15) from both the 5′- and the 3′-ends were trimmed by using btrim [42]. reads were aligned to the reference genome of btx623 (sbicolor_v1.4_79) [43] by using tophat version 2.0.4 [44]. differentially expressed genes were identified by using cuffdiff version […]

2018
PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] the primerid from each read, with options—post ca—removepost, and place the primerid sequence in the sequence id line for each read. each fastq file was split into separate amplicon libraries using btrim64[46] with options -u 2 -v 2 -s -b -e 300; a list of primers for each amplicon was also supplied. off-target sequences were removed with get_majority_block_bam.pl, a wrapper script that maps […]

2018
PMCID: 5845675
PMID: 29559963
DOI: 10.3389/fmicb.2018.00381

[…] recommendations. sequencing was performed in the illumina nextseq 500., clean data were obtained from the raw data by removing the sequences of the adapters and low-quality reads using btrim64-static (kong, 2011). the clean reads were aligned to the a. massiliensis f0489 genome (genbank accession number: akft00000000) using star with default parameters, allowing up to one-base […]

2018
PMCID: 5919721
PMID: 29620157
DOI: 10.3892/ijo.2018.4336

[…] san diego, ca, usa)., fastqc (version 0.11.5) was used to assess the sequence length distribution and quality of the ngs data, as previously described (22). adaptor sequences were trimmed using btrim, and all reads without adaptors were discarded (23). additionally, reads shorter than 15 nt were excluded from the data set (24). prior to mirna analysis, reads pertaining to ribosomal rna […]

2017
PMCID: 5446123
PMID: 28552958
DOI: 10.1371/journal.pone.0177664

[…] kit v3 (illumina). sequencing was performed over 50 cycles on a hiseq 2500 sequencer., adapter sequences, excessively short reads and low quality reads were trimmed from the raw sequence data using btrim [19]. the trimmed reads were aligned to the equine genome assembly equ cab 2.0 using bowtie2 [20] in end-to-end mode, with a seed length of 14 nucleotides, allowing no mismatches. reads mapping […]

Btrim institution(s)
Department of Molecular Biophysics and Biochemistry, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA

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