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

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.

GenoViewer 0.9.0 – Viewer/Browser for the Sam/Bam format

GenoViewer 0.9.0

:: DESCRIPTION

GenoViewer is a comprehensive and open source viewer/browser for the sam/bam format commonly used in the assembly tasks of Next Generation Sequencing data.

::DEVELOPER

Astrid Research, Inc.

:: SCREENSHOTS

GenoViewer

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java 

:: DOWNLOAD

 GenoViewer

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(2):107-9. Epub 2012 Jan 20.
Geno viewer, a SAM/BAM viewer tool.
Laczik M, Tukacs E, Uzonyi B, Domokos B, Doma Z, Kiss M, Horváth A, Batta Z, Maros-Szabó Z, Török Z.

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

SAM 4.01 – Significance Analysis of Microarrays

SAM 4.01

:: DESCRIPTION

SAM (Significance Analysis of Microarrays) is a statistical technique for finding significant genes in a set of microarray experiments, a supervised learning software for genomic expression data mining.

The input to SAM is gene expression measurements from a set of microarray experiments, as well as a response variable from each experiment. The response variable may be a grouping like untreated, treated [either unpaired or paired], a multiclass grouping (like breast cancer, lymphoma, colon cancer, . . . ), a quantitative variable (like blood pressure) or a possibly censored survival time.

::DEVELOPER

Stanford University Statistics and Biochemistry Labs

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SAM

:: MORE INFORMATION

Citation

Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.

samcomp 0.9 – Compression for SAM/BAM file format

samcomp 0.9

:: 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

Quip 1.1.8 – Aggressive Compression of FASTQ and SAM/BAM files

Quip 1.1.8

:: DESCRIPTION

Quip compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.

::DEVELOPER

Daniel C. Jones

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Quip

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Dec;40(22):e171. doi: 10.1093/nar/gks754. Epub 2012 Aug 16.
Compression of next-generation sequencing reads aided by highly efficient de novo assembly.
Jones DC, Ruzzo WL, Peng X, Katze MG.

Samscope 1.6.6.91 – Lightweight SAM/BAM File Viewer

Samscope 1.6.6.91

:: DESCRIPTION

Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun!Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ features like polarity. The paging-friendly binary file layout makes it feasible to browse data sets far larger than the system’s available RAM.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

Samscope

:: REQUIREMENTS

  • Linux 

:: DOWNLOAD

 Samscope

:: MORE INFORMATION

Citation

Bioinformatics. 2012 May 1;28(9):1276-7. doi: 10.1093/bioinformatics/bts122. Epub 2012 Mar 13.
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
Popendorf K, Sakakibara Y.

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