Btrim statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Btrim
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Tool usage distribution map

This map represents all the scientific publications referring to Btrim per scientific context
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Protocols

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

Versioning


No version available

Publication for Btrim

Btrim citations

 (51)
call_split

A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana

2018
Front Plant Sci
PMCID: 5838922
PMID: 29545818
DOI: 10.3389/fpls.2018.00265
call_split See protocol

[…] rated 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 […]

library_books

Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype specific salt tolerance mechanisms

2018
BMC Plant Biol
PMCID: 5815232
PMID: 29448940
DOI: 10.1186/s12870-018-1250-4

[…] s were 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, and be […]

library_books

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs

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

[…] t 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 the r […]

library_books

Root lodging is a physical stress that changes gene expression from sucrose accumulation to degradation in sorghum

2018
BMC Plant Biol
PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] NAs [, ] and 100-bp reads were obtained by using an Illumina Hiseq2000 sequencer (Illumina, San Diego, CA, USA). Low-quality nucleotides (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 [] […]

call_split

LRRTM1 underlies synaptic convergence in visual thalamus

2018
eLife
PMCID: 5826289
PMID: 29424692
DOI: 10.7554/eLife.33498.020
call_split See protocol

[…] equenced 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 […]

call_split

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

2017
Front Microbiol
PMCID: 5681905
PMID: 29163453
DOI: 10.3389/fmicb.2017.02179
call_split See protocol

[…] . Firstly, 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, r […]


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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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