BamTools statistics

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Citations per year

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

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

BamTools specifications

Information


Unique identifier OMICS_11315
Name BamTools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, BED
Output format SAM, BAM, BED, BAI
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Derek Barnett

Publication for BamTools

BamTools citations

 (74)
library_books

Haplotype Based Genotyping in Polyploids

2018
Front Plant Sci
PMCID: 5932196
PMID: 29755500
DOI: 10.3389/fpls.2018.00564

[…] polymorphisms were then used as a guide for the haplotyping procedure. The program is written in C++ as a standalone program. To access bam files and retrieve reads aligned to specific locations, the bamtools API is used (). First, all haplotypes for each accession are collected at every two-position haplotype where there is a potential polymorphism at both sites within a specified base window. Ha […]

library_books

Single cell full length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

2018
Nat Commun
PMCID: 5809388
PMID: 29434199
DOI: 10.1038/s41467-018-02866-0

[…] paRNA-seq data. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.1) with parameters “--dta-cufflinks -p 4 -k 5 --sp 1000,1000.” Uniquely mapped reads were selected using the BAMtools (version 2.0.1) “filter” command with the parameters “-isMapped true -tag NH:1” and the SAMTools (version 2.0.1) “view” command with the parameter “-q 40.” BEDTools (version 2.22.1) and R wer […]

library_books

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

2017
Ecol Evol
PMCID: 5792620
PMID: 29435226
DOI: 10.1002/ece3.3699

[…] y of being damaged using mapDamage V2.0 (Jónsson, Ginolhac, Schubert, Johnson, & Orlando, ). We sorted the aligned reads of each individual according to their position on the reference catalogue with BamTools (Barnett, Garrison, Quinlan, Strömberg, & Marth, ), and we excluded PCR duplicates by eliminating fragments starting and ending at the same positions using SAMtools V0.1.19 (Li et al., ).For […]

call_split

Piperlongumine potentiates the effects of gemcitabine in in vitro and in vivo human pancreatic cancer models

2017
Oncotarget
PMCID: 5828188
PMID: 29535819
DOI: 10.18632/oncotarget.23623
call_split See protocol

[…] lus.GRCm38) downloaded from Ensembl. The raw fastq data were subjected to quality trimming using Sickle, for a minimum length of 50. HISAT2 [] was used to map the reads on the genome. SAMtools [] and BAMtools [] were used to convert and sort the BAM files. HTSeq [] was used to count the reads. […]

library_books

Reference guided de novo assembly approach improves genome reconstruction for related species

2017
BMC Bioinformatics
PMCID: 5681816
PMID: 29126390
DOI: 10.1186/s12859-017-1911-6

[…] of Bowtie2 and calculated the percentage of mapped reads, mapped reads with a mapping quality > = 10 and the percentage of proper paired reads with a mapping quality > = 10 using samtools v0.1.19 and bamTools v2.3.0 []. We calculated the scaffold NG50 and the error corrected NG50 using GAGE. The error corrected NG50 corresponds to the NG50 value computed on sequences broken at each misassembly. Ad […]

call_split

Combating subclonal evolution of resistant cancer phenotypes

2017
Nat Commun
PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3
call_split See protocol

[…] rg/cms/index.php?page=trimmomatic). Alignment to hg19 was done with BWA MEM v0.7.8 (https://github.com/lh3/bwa). BAM files were refined using PicardTools’ MarkDuplicates and FixMateInformation tools, BamTools filter tool (https://github.com/pezmaster31/bamtools), and GATK’s RealignerTargetCreator, IndelRealigner, and BaseRecalibrator (v3.2-2; https://www.broadinstitute.org/gatk/download/). WES som […]


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BamTools institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA; Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA; Illumina, Inc, San Diego, CA, USA
BamTools funding source(s)
National Institutes of Health grants (RO1 HG004719 and RC2 HG005552)

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