:: DESCRIPTION
BiSSAP is a computer program designed to facilitate the creation of sequence listings for patent applications containing biological sequences (see Rule 30 EPC, Rule 5.2 PCT, and the Decision of the President and Notice from the EPO dated 28 April 2011 (OJ EPO 6/2011, 372 ff.)).
::DEVELOPER
EPO BiSSAP Team (bissap@epo.org)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
fastq Merger will merge fastqs with the GSL naming convention by their library IDs.
::DEVELOPER
The HudsonAlpha Genomic Services Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
:: DESCRIPTION
SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
libCSAM will contain several C++ codes for compress,decompress, and access each of the fields of any SAM format file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 2.
Lossy compression of quality scores in genomic data.
Cánovas R1, Moffat A, Turpin A.
:: 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
FastqCLS is a robust FASTQ-specific compressor for recent generation data via score-based reordering.
:: DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lee D, Song G.
FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model.
Bioinformatics. 2021 Oct 8:btab696. doi: 10.1093/bioinformatics/btab696. Epub ahead of print. PMID: 34623374.
:: DESCRIPTION
fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression.
Fqzcomp is a basic fastq compressor, designed primarily for high performance.
::DEVELOPER
:: 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
bwtool is a command-line utility for bigWig files. BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth).
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 1;30(11):1618-9. doi: 10.1093/bioinformatics/btu056. Epub 2014 Jan 30.
bwtool: a tool for bigWig files.
Pohl A, Beato M.
:: DESCRIPTION
GBKParser, a simple tool for parsing basic gene information from a genbank file.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA.
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Res, 35, W522-5, 2007.
