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.

DeeZ 1.9-beta2 – A tool for Compressing SAM/BAM files

DeeZ 1.9-beta2

:: DESCRIPTION

DeeZ (a.k.a. DeeNA-Zip) is a tool for compressing SAM/BAM files, or more formally, a tool which does reference-based compression by local assembly

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DeeZ

:: MORE INFORMATION

Citation

DeeZ: reference-based compression by local assembly.
Hach F, Numanagić I, Sahinalp SC.
Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133.

Sambamba 0.6.1 – Tools for working with SAM/BAM data

Sambamba 0.6.1

:: DESCRIPTION

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.

::DEVELOPER

Sambamba team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOSX

:: DOWNLOAD

 Sambamba

:: MORE INFORMATION

Citation

Sambamba: fast processing of NGS alignment formats.
Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P.
Bioinformatics. 2015 Feb 19. pii: btv098.

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;

rbamtools 2.12.3 – An R package for Reading and Writing BAM (Binary Alignment) files

rbamtools 2.12.3

:: DESCRIPTION

rbamtools provides an interface to functions of the ‘SAMtools‘ C-Library by Heng Li.

::DEVELOPER

Wolfgang Kaisers <kaisers at med.uni-duesseldorf.de>

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 rbamtools

:: MORE INFORMATION

Citation:

rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.
Kaisers W, Schaal H, Schwender H.
Bioinformatics. 2015 Jan 5. pii: btu846

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

BamHash 1.0 – Hash BAM and FASTQ files to verify Data Integrity

BamHash 1.0

:: DESCRIPTION

BamHash is a checksum program for verifying the integrity of sequence data.

::DEVELOPER

Decode Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

   BamHash

:: MORE INFORMATION

Citation:

BamHash: a checksum program for verifying the integrity of sequence data.
óskarsdóttir A, Másson G, Melsted P.
Bioinformatics. 2015 Sep 10. pii: btv539.

BioAssemblyModeler (BAM) 2.0.14.0 – Homology Modeling of Protein Homo- and Heterooligomers

BAM 2.0.14.0

:: DESCRIPTION

BioAssemblyModeler (BAM) is a graphical user interface (GUI) application for building protein homooligomers and heterooligomers by means of comparative (homology) modeling.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

BAM

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BAM

:: MORE INFORMATION