BamView protocols

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BamView specifications

Information


Unique identifier OMICS_00878
Name BamView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Tim Carver <>

Publications for BamView

BamView in pipelines

 (5)
2015
PMCID: 4491227
PMID: 26141822
DOI: 10.1186/s12864-015-1661-7

[…] using bowtie v2 on the biolinux platform [, ]. approximately 97 % of reads aligned for each sequencing run (additional file : table s1). aligned reads were visualized using artemis with the bamview plugin []. raw read counts for each gene were tabulated (additional file : table s2) using bedtools and also used to calculate a reads per kilobase coding sequence per million sequenced reads […]

2014
PMCID: 3916515
PMID: 24410969
DOI: 10.1186/1471-2164-15-20

[…] only the reads that match 100% to the reference. the sam output from bowtie was converted binary file (bam) using samtools. the bam output was then used to generate the alignment map using the bamview program. for the conservation analysis between the pericentromeric regions of the sex chromosomes, we manually extracted the srna hotspots from each chromosomes based on the alignment maps […]

2014
PMCID: 4223743
PMID: 25344729
DOI: 10.1186/1471-2164-15-938

[…] and altde1 strains. remaining reads were subsequently mapped to the altde and altde1 chromosome sequence with the default parameters. samtools [] were used to convert resulting data into bam format. bamview [] was subsequently used for the visualization of the sequence reads against the altde and altde1 genomes. once the transcripts were mapped to the genomes, the expression values of genes […]

2013
PMCID: 3814198
PMID: 24029811
DOI: 10.1093/gbe/evt140

[…] reads per kilobase of exon model per million mapped reads (rpkm) values () separately for sense and antisense reads mapped to the insert region and flanking genes using artemis v. 15.1.1 () and bamview v. 1.2.9 ()., sequencing and assembly of a 158,719-bp a. syriaca plastome (genbank: kf386166) confirmed a 2,427-bp insertion in the rps2–rpoc2 intergenic spacer (2,677 bp total length; a) […]

2013
PMCID: 4357781
PMID: 23665476
DOI: 10.1016/j.gpb.2013.03.001

[…] sirna were produced in phase, reads from each library were mapped against the candidate loci as described above. sam files obtained from mapping were converted and visualized using samtools and bamview ., all non-redundant reads mapping to a candidate ta-sirna loci were used to screen for targets against annotated genes in the cassava genome. target prediction was performed using […]


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BamView in publications

 (17)
PMCID: 5751559
PMID: 29297355
DOI: 10.1186/s12859-017-1897-0

[…] intergenic regions whose expression was influenced by the rnase iii gene deletion., this analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. using artemis and bamview genome viewers, these regions were visually verified leaving 6 putative srnas. this study not only expanded our knowledge on novel srnas but would also give us new insight into srna […]

PMCID: 5478719
PMID: 28680429
DOI: 10.3389/fpls.2017.01023

[…] onto the quinoa reference genome, we chose only quinoa accessions for cnv analysis. we also manually confirmed cnvs by comparing the differences in mapped reads between different samples using the bamview tool (ver 1.2.11) (carver et al., )., to identify snps potentially related to the differences in salinity tolerance of the accessions, snps were called in each of the 219 candidate genes […]

PMCID: 5290327
PMID: 28139658
DOI: 10.1038/ncomms14193

[…] ools package. a bespoke perl script returns genes where just drug-resistant sample had single-nucleotide polymorphisms. last, large deletions, insertions and duplications were manually detected using bamview., trophozoite-stage p. falciparum hb3 parasites were incubated with 10 μm of fluo-4-am in rpmi 1640 medium (life technologies) with pluoronic f-127 (0.1% (v/v)) and 40 μm of probenecid for 40  […]

PMCID: 4927586
PMID: 27446065
DOI: 10.3389/fmicb.2016.01037

[…] (li et al., ). the sam file was converted to a binary bam file, sorted and indexed by using the “view,” “sort” and “index” functions of samtools, respectively. the bam file was checked using the bamview tool and used for variation report generation (carver et al., ). the consensus sequence was generated using samtools. the variation report in “bcf” format was converted into a “vcf” file […]

PMCID: 4756669
PMID: 26884212
DOI: 10.1038/srep21121

[…] annotation information for a. oleivorans dr1 was obtained from the national center for biotechnology information (ncbi) database (accession number nc_014259.1). mapped reads were visualized using bamview and artemis software. the rna-seq data were deposited in the ncbi gene expression omnibus site under accession number gse44347 (exponential and stationary phase grown in nb medium) […]


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BamView institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
BamView funding source(s)
Wellcome Trust through their funding of the Pathogen Genomics group at the Wellcome Trust Sanger Institute (WT 085775/Z/08/Z)

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