Btrim protocols

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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

 (14)
2018
PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] [, ] 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 []. reads were aligned to the reference genome of btx623 (sbicolor_v1.4_79) [] by using tophat version 2.0.4 []. differentially expressed genes were identified by using cuffdiff version 2.2.0 […]

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[] 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 (). 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 mismatches (). […]

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

[…] inc., 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 (). adaptor sequences were trimmed using btrim, and all reads without adaptors were discarded (). additionally, reads shorter than 15 nt were excluded from the data set (). prior to mirna analysis, reads pertaining to ribosomal rna (rrna), […]

2017
PMCID: 5325256
PMID: 28234939
DOI: 10.1371/journal.pone.0172220

[…] cell was loaded with each 12 mc and 12 sm samples to assure reproducible conditions., the resulting data was processed using an in-house procedure []. adaptor sequences were trimmed from 3’end with btrim []. the sequence data quality control software fastqc (babraham bioinformatics, uk, version 0.10.1) was used to calculate length distribution and representing base calling accuracy by the phred […]


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Btrim in publications

 (49)
PMCID: 5919721
PMID: 29620157
DOI: 10.3892/ijo.2018.4336

[…] inc., 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 (). adaptor sequences were trimmed using btrim, and all reads without adaptors were discarded (). additionally, reads shorter than 15 nt were excluded from the data set (). prior to mirna analysis, reads pertaining to ribosomal rna (rrna), […]

PMCID: 5838922
PMID: 29545818
DOI: 10.3389/fpls.2018.00265

[…] from each bulked pool, comprising 104 million reads for the virulent bulk and 110 million reads for the avirulent bulk. the illumina reads were first trimmed based on their quality scores using btrim (kong, ) with a cut-off of 25 for average quality scores within a moving window of 5 bp. the minimum acceptable read length was 25 bp (that is, reads that were shorter than 25 bp after trimming […]

PMCID: 5815232
PMID: 29448940
DOI: 10.1186/s12870-018-1250-4

[…] cleaned by removing adapters and low-quality sequences (reads with ambiguous bases ‘n’ and reads with more than 10% q < 20 bases) with cutadapt (https://cutadapt.readthedocs.io/en/stable/) and btrim []. the cleaned reads were mapped to the reference genome of m. truncatula (mt 4.0), but the mapping ratio was lower than 50%, probably due to the highly heterozygous genome of m. sativa, […]

PMCID: 5826289
PMID: 29424692
DOI: 10.7554/eLife.33498.020

[…] 2 × 100 pe using truseq sbs kit v3-hs (200-cycles) (cat # fc-401–3001). low-quality base calls, sequences with low-complexity tails, and adaptor sequences were removed using a combination of btrim and ea-utils. sequencing reads were then aligned to the mouse genome (tophat2/bowtie) and expression determined via htseq counting. deseq2 has been used to determine fold change and statistical […]

PMCID: 5681905
PMID: 29163453
DOI: 10.3389/fmicb.2017.02179

[…] reads were assigned to different samples according to their barcode sequences and primer sequences were then removed. subsequently, low quality reads (qc threshold < 20) were removed using btrim (). then, the forward and reverse reads with at least 10 bp overlap and less than 5% mismatches were merged using flash (), ambiguous bases (n) were removed from the merged sequences. finally, […]


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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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