Tag: BAM

BamView 1.2.11 – Display of Read Alignments in BAM Data Files

BamView 1.2.11

:: DESCRIPTION

BamView is a free interactive display of read alignments in BAM data files.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

BamView

:: MORE INFORMATION

Citation

Brief Bioinform. 2013 Mar;14(2):203-12. doi: 10.1093/bib/bbr073. Epub 2012 Jan 16.
BamView: visualizing and interpretation of next-generation sequencing read alignments.
Carver T1, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA.

Tim Carver; Ulrike Böhme, Thomas D. Otto; Julian Parkhill; Matthew Berriman
BamView: Viewing mapped read alignment data in the context of the reference sequence.
Bioinformatics 2010;

CBrowse 1.11 – SAM/BAM-based Contig Browser for Transcriptome Assembly

CBrowse 1.11

:: DESCRIPTION

CBrowse (Contig Browser) is a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.  It takes the contig sequence file and its relevant SAM/BAM file as the input, processes the input data, detects polymorphisms and repeats, and generates image, JSON and MySQL-compatible text files that can be directly utilized by different viewers of CBrowse.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CBrowse

:: MORE INFORMATION

Citation:

Pei Li, Guoli Ji, Min Dong, Emily Schmidt, Douglas Lenox, Liangliang Chen, Qi Liu, Lin Liu, Jie Zhang and Chun Liang (2012)
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Bioinformatics, doi: 10.1093/bioinformatics/bts443

bamUTIL 1.0.14 – Perform Operations on SAM/BAM files

bamUTIL 1.0.14

:: DESCRIPTION

bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 bamUTIL

:: MORE INFORMATION

Gambit 0.4.145 – Graphical BAM Alignment Viewer

Gambit 0.4.145

:: DESCRIPTION

Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis.The software takes advantage of the indexing features of the (fairly) recently standardized BAM sequence alignment format that allows rapid access to genomic data, with minimal startup time and re-rendering delay. Gambit also supports a variety of annotation formats (BED, GFF, GFF3, VCF) “out-of-the-box” for displaying gene/region annotations as well as SNP entries.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 Gambit

:: MORE INFORMATION

Mosdepth v0.2.6 – Fast BAM/CRAM Depth Calculation for WGS, Exome, or Targeted Sequencing

Mosdepth v0.2.6

:: DESCRIPTION

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Mosdepth

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.
Mosdepth: quick coverage calculation for genomes and exomes.
Pedersen BS, Quinlan AR.

BamTable 0.1.2 – a rapid BAM file Filter

BamTable 0.1.2

:: DESCRIPTION

BamTable filters sorted bam files according to a configurable set of criteria and prints a table with the number of A, C, G and T bases that passed filtering for each position in the selected range.

::DEVELOPER

Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  BamTable

:: MORE INFORMATION

BAMseek 20110724 – Browse Large BAM and SAM Alignment Files

BAMseek 20110724

:: DESCRIPTION

Bamseek provides easy-to-use user interface to browse files too large to be opened with conventional text editors, such as TextEdit or Word. Supports SAM/BAM, VCF (BGZF-compressed and uncompressed), and FASTQ formats.

::DEVELOPER

Justin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 BAMseek

:: MORE INFORMATION