Tag: ASAP

ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

ASAP – Assemble Species by Automatic Partitioning

ASAP

:: DESCRIPTION

ASAP is a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets).

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Puillandre N, Brouillet S, Achaz G.
ASAP: assemble species by automatic partitioning.
Mol Ecol Resour. 2021 Feb;21(2):609-620. doi: 10.1111/1755-0998.13281. Epub 2020 Nov 20. PMID: 33058550.

ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time

ASAP 0.1.2

:: DESCRIPTION

ASAP(Allele-specific Alignment Pipeline) is a program to align a sequencing file to two genomes at the same time. This can be useful to detect allelic imbalances in samples which are of different genetic origin. Examples would be studying imprinted regions in ChIP-Seq or RNA-Seq experiments, or genomic interactions (e4C) in mouse strains with a mixed genetic background.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

ASAP 1.4.1 – A Systematic Annotation Package for Community Analysis of Genomes

ASAP 1.4.1

:: DESCRIPTION

ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data.

::DEVELOPER

Genome Evolution Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • PHP
  • MySQL

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2003 Jan 1;31(1):147-51.
ASAP, a systematic annotation package for community analysis of genomes.
Glasner JD1, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT.

Asap – Promoter Analysis

Asap

:: DESCRIPTION

Asap is an open source framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

asap

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 Asap

:: MORE INFORMATION

Citation:

Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A:
Asap: a framework for over-representation statistics for transcription factor binding sites.
PLoS ONE 2008, 3(2):e1623