:: DESCRIPTION
SamQL is a structured query language and filtering tool for the SAM/BAM file format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lee CT, Maragkakis M.
SamQL: a structured query language and filtering tool for the SAM/BAM file format.
BMC Bioinformatics. 2021 Oct 2;22(1):474. doi: 10.1186/s12859-021-04390-3. PMID: 34600480; PMCID: PMC8487582.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
SAM (Sequence Assembly Manager)is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.
::DEVELOPER
Canada’s Michael Smith Genome Sciences Centre
:: SCREENSHOTS
: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. (2005)
Management and Visualization of Whole Genome Shotgun Assemblies using SAM.
Biotechniques. 38:715-720
:: 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
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Quip compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
