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chevron_left File indexation Known transcript quantification File format conversion File merging Duplicate read removal File filtering Depth of coverage File sorting chevron_right
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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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Maintainer


  • person_outline Derek Barnett <>

Publication for BamTools

BamTools in pipelines

 (23)
2018
PMCID: 5878685
PMID: 29610759
DOI: 10.15698/mic2018.04.623

[…] in supplemental table s5., illumina reads were aligned to the s. pombe genome assembly asm294v2.23 using bowtie v2.1.0 with default parameters and multi-mapper reads randomly distributed. using bamtools , read counts were normalized to reads per million per kilo base (rpkm), using the total library size and a bin size of 1 kb. for the analysis of multi-mapper reads, we filtered aligned read […]

2017
PMCID: 5310062
PMID: 28201993
DOI: 10.1186/s12864-017-3560-6

[…] paper []., for coverage curves illustrating deletion of crispr-dr-cas regions that were present in the template h37rv chromosome sequence, the aligned bam files were converted to wig files using bamtools, bedtools, and ucsc-tools. the wig files were imported into ucsc microbial genome viewer (http://microbes.ucsc.edu)., recovery of spoligotypes from ngs data was accomplished as follows. […]

2017
PMCID: 5472622
PMID: 28620196
DOI: 10.1038/s41598-017-03837-z

[…] background model. we defined those entries with p-value ≤ 0.05 as the significantly differential methylated compared with background model., bowtie2 was used to align sequencing reads, samtools and bamtools were used to process the aligned sequencing reads, methylkit was used to analyze part of rrbs data, and deseq was used to analyze rna-seq data., integration of multi-platform […]

2017
PMCID: 5506248
PMID: 28713572
DOI: 10.1038/hortres.2017.32

[…] (http://ccb.jhu.edu/software/tophat/manual.shtml). intermediary processing of the mapped reads (sam and bam files) such as read deduplication and read group renaming was done using samtools, bamtools and picardtools., once aligned, the count data required by edger were obtained as a sum of overlapping reads on the annotated gene feature (gff3 file) using htseq. differential gene […]

2017
PMCID: 5660447
PMID: 29078748
DOI: 10.1186/s12864-017-4230-4

[…] and then the remaining sequences were formatted with sammap.pl script with reference to map.psl. the mapped results of the miseq reads on b. ovata were further filtered to remove n nucleotides with bamtools with operation n filter.txt script in the augustus package. the filtered and mapped results were merged with those for spliced reads annotated as above. another intron file, hints 2, […]


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BamTools in publications

 (67)
PMCID: 5932196
PMID: 29755500
DOI: 10.3389/fpls.2018.00564

[…] 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. […]

PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] v1.0.6 []., both haddock and cod were sequenced in the [] study, and these 150 bp reads were mapped to the respective assemblies using bwa mem v0.7.12 [], and sorted using samtools v0.1.19 []. bamtools v2.3.0 and the script ‘coverage_to_regions.py’ from freebayes v0.9.14 [] were used to split the assembly into regions, and freebayes was run in parallel. vcflib from a github snapshot […]

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

[…] 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 […]

PMCID: 5874624
PMID: 29361673
DOI: 10.3390/microorganisms6010010

[…] technologies, loughborough, uk). generated sequence data was mapped to the reference sequence data (cp001050; []) using galaxy. the ion torrent bam format files were converted to fastq format using bamtools convert []. fastq groomer was used on all ngs data []. bowtie2 was used to map the reads against the reference [,] before visualization using the integrated genomics viewer (igv) [,]. […]

PMCID: 5792620
PMID: 29435226
DOI: 10.1002/ece3.3699

[…] 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., […]


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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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