bamstats 0.4
:: DESCRIPTION
bamstats is a program to extract various information from BAM alignmnet files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- Haskell Platform
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
bamstats is a program to extract various information from BAM alignmnet files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
BamHash is a checksum program for verifying the integrity of sequence data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
BioAssemblyModeler (BAM) is a graphical user interface (GUI) application for building protein homooligomers and heterooligomers by means of comparative (homology) modeling.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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
:: 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
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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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.