BamView pipeline

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

Versioning


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Maintainer


  • person_outline Tim Carver <>

Publications for BamView

BamView IN pipelines

 (3)
2015
PMCID: 4491227
PMID: 26141822
DOI: 10.1186/s12864-015-1661-7

[…] using bowtie v2 on the biolinux platform [15, 16]. approximately 97 % of reads aligned for each sequencing run (additional file 1: table s1). aligned reads were visualized using artemis with the bamview plugin [17]. raw read counts for each gene were tabulated (additional file 2: table s2) using bedtools and also used to calculate a reads per kilobase coding sequence per million sequenced […]

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

[…] altde1 strains. remaining reads were subsequently mapped to the altde and altde1 chromosome sequence with the default parameters. samtools [51] were used to convert resulting data into bam format. bamview [52] 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

[…] million mapped reads (rpkm) values (mortazavi et al. 2008) separately for sense and antisense reads mapped to the insert region and flanking genes using artemis v. 15.1.1 (carver et al. 2012) and bamview v. 1.2.9 (carver et al. 2013)., 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 […]

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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