pyGenClean 1.8.3 – Tool for Genetic Data Clean up before Association Testing

pyGenClean 1.8.3

:: DESCRIPTION

pyGenClean is an informatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjuction with a source batch-queuing system, the tool minimizes data manipulation errors, it accelerates the completion of the data clean up process and it provides informative graphics and metrics to guide decision making for statistical analysis.

::DEVELOPER

Marie-Pierre Dubé’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Python

:: DOWNLOAD
 pyGenClean

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 30. [Epub ahead of print]
pyGenClean: efficient tool for genetic data clean up before association testing.
Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, Dubé MP.

FASTAFS v1.8.0 – File System Virtualisation of Random Access Compressed FASTA files

FASTAFS v1.8.0

:: DESCRIPTION

FASTAFS is a user-friendly and easy to deploy backwards compatible generic purpose solution to store and access compressed FASTA files, since it offers file system access to FASTA files as well as in-sync metadata files through file virtualisation.

::DEVELOPER

Youri Hoogstrate

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FASTAFS

:: MORE INFORMATION

Citation

Hoogstrate Y, Jenster GW, Werken HJGV.
FASTAFS: file system virtualisation of random access compressed FASTA files.
BMC Bioinformatics. 2021 Nov 1;22(1):535. doi: 10.1186/s12859-021-04455-3. PMID: 34724897.

SPRING v1.0.1 – FASTQ Compressor

SPRING v1.0.1

:: DESCRIPTION

SPRING is a compression tool for Fastq files.

::DEVELOPER

Tsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda
  • C COmpiler

:: DOWNLOAD

SPRING

:: MORE INFORMATION

Citation

Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T.
SPRING: a next-generation compressor for FASTQ data.
Bioinformatics. 2019 Aug 1;35(15):2674-2676. doi: 10.1093/bioinformatics/bty1015. PMID: 30535063; PMCID: PMC6662292.

QualComp – Lossy Compression algorithm for Quality Scores

QualComp

:: DESCRIPTION

QualComp is a lossy compression algorithm for the quality scores presented in a FASTQ file.

::DEVELOPER

Tsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C COmpiler

:: DOWNLOAD

QualComp

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jun 8;14:187. doi: 10.1186/1471-2105-14-187.
QualComp: a new lossy compressor for quality scores based on rate distortion theory.
Ochoa I1, Asnani H, Bharadia D, Chowdhury M, Weissman T, Yona G.

fqCleanER 21.10 – Fastq Cleaning and Enhancing Routine

fqCleanER 21.10

:: DESCRIPTION

fqCleanER is a command line tool to ease the different standard preprocessing steps of short high-throughput sequencing (HTS) reads.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOsX

:: DOWNLOAD

fqCleanER

:: MORE INFORMATION

bam2fastq 1.1.0 – Extract Sequences from a BAM file in Fastq format

bam2fastq 1.1.0

:: DESCRIPTION

bam2fastq is a program to extract sequences and qualities from a BAM file.

::DEVELOPER

The Genomic Services Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
:: DOWNLOAD

 bam2fastq

:: MORE INFORMATION

SFF Workbench 1.5.1 – Simple SFF File Editor & Converter

SFF Workbench 1.5.1

:: DESCRIPTION

SFF Workbench (Standard flowgram format , SFF Tools) is an easy to use SFF file viewer, editor and converter. It is the first and only SFF editor with graphic interface on the entire bioinformatics market! With this tool we wanted to help the biologists to concentrate on their work instead of wasting time poking commands in an obscure text console.

The Roche/454 platform produces sequence reads in SFF format. SFF file contains the flow grams and quality scores for each read in addition to other information.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SFF Workbench

:: MORE INFORMATION

BiSSAP 1.3 – Biological Sequence Submission Application for Patents

BiSSAP 1.3

:: 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

BiSSAP

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 BiSSAP

:: MORE INFORMATION