samcomp 0.10 – Compression for SAM/BAM file format

samcomp 0.10

:: DESCRIPTION

samcomp is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.

::DEVELOPER

James K. Bonfield (jkb@sanger.ac.uk), Matt Mahoney

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 samcomp

:: MORE INFORMATION

 Citation

Bonfield JK, Mahoney MV (2013)
Compression of FASTQ and SAM Format Sequencing Data. 
PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190

bamchop – Generate Targeted Resequencing Report from BAM File

bamchop

:: DESCRIPTION

bamchop is a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report.

::DEVELOPER

The Department of Biomedical and Health Informatics (DBHi)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • R
  • LaTeX

:: DOWNLOAD

 bamchop

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 11:S3. doi: 10.1186/1471-2105-14-S11-S3. Epub 2013 Sep 13.
Efficient digest of high-throughput sequencing data in a reproducible report.
Zhang Z, Leipzig J, Sasson A, Yu AM, Perin JC, Xie HM, Sarmady M, Warren PV, White PS.

BamHash 2.0 – Hash BAM and FASTQ files to verify Data Integrity

BamHash 2.0

:: 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) 2.1.0.2 – Homology Modeling of Protein Homo- and Heterooligomers

BAM 2.1.0.2

:: 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

rbamtools 2.16.17 – An R package for Reading and Writing BAM (Binary Alignment) files

rbamtools 2.16.17

:: 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

Sambamba 0.8.0 – Tools for working with SAM/BAM data

Sambamba 0.8.0

:: 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.

Alfred v0.2.3 – BAM Alignment Statistics, Feature Counting and Annotation

Alfred v0.2.3

:: DESCRIPTION

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments

::DEVELOPER

Tobias Rausch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alfred

:: MORE INFORMATION

Citation:

Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.

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.

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;