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Citations per year

Number of citations per year for the bioinformatics software tool BamTools

Tool usage distribution map

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

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BamTools specifications


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




No version available



  • person_outline Derek Barnett

Publication for BamTools

BamTools citations


Haplotype Based Genotyping in Polyploids

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 […]


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

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

[…] SAT2 with the parameters “--dta-cufflinks --rna-strandness RF -k 5 --no-mixed --no-discordant --sp 1000,1000.” Properly (i.e., convergent read pairs) and uniquely mapped reads were selected using the BAMtools “filter” command and SAMTools “view” command with the parameter “-q 40.” For genome-guided transcriptome assembly, Cufflinks was used with the parameters “--multi-read-correct --frag-bias-cor […]


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

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 […]


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

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. […]


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

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 […]


Combating subclonal evolution of resistant cancer phenotypes

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 ( BAM files were refined using PicardTools’ MarkDuplicates and FixMateInformation tools, BamTools filter tool (, and GATK’s RealignerTargetCreator, IndelRealigner, and BaseRecalibrator (v3.2-2; 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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