OMGS – Optical Map-Based Genome Scaffolding

OMGS

:: DESCRIPTION

OMGS is a fast genome scaffolding tool which takes advantage of one or multiple Bionano optical maps to accurately generate scaffolds.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

OMGS

:: MORE INFORMATION

Citation

Pan W, Jiang T, Lonardi S.
OMGS: Optical Map-Based Genome Scaffolding.
J Comput Biol. 2020 Apr;27(4):519-533. doi: 10.1089/cmb.2019.0310. Epub 2019 Dec 3. PMID: 31794680.

MetaObtainer – Obtaining the Specified Species from NGS short reads

MetaObtainer

:: DESCRIPTION

MetaObtainer is a tool for obtaining the specified species from next-generation sequencing short reads.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaObtainer

:: MORE INFORMATION

Citation

Pan W, Chen B, Xu Y.
MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.
Interdiscip Sci. 2015 Dec;7(4):405-13. doi: 10.1007/s12539-015-0281-x. Epub 2015 Aug 21. PMID: 26293485.

BRAT 1.2.4 / BRAT-BW 2.0.1 / BRAT-nova – Bayesian Modeling of Recombination Events

BRAT 1.2.4 / BRAT-BW 2.0.1 / BRAT-nova

:: DESCRIPTION

BRAT contains an implementation of a Bayesian model-based method for detecting recombination events in bacterial populations using DNA sequence data.

BRAT-BW is a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform).

BRAT-nova is a novel optimized versatile aligner that is accurate and fast. BRAT-nova is faster than BRAT-BW. BRAT-nova maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). The package includes tools for trimming low quality read ends and for counting methylation level.

::DEVELOPER

Algorithms and Computational Biology Lab ,University of California / Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 BRAT

:: MORE INFORMATION

Citation:

Harris EY, Ounit R, Lonardi S.
BRAT-nova: fast and accurate mapping of bisulfite-treated reads.
Bioinformatics. 2016 Sep 1;32(17):2696-8. doi: 10.1093/bioinformatics/btw226. Epub 2016 Apr 23. PMID: 27153660.

Bioinformatics. 2012 Jul 1;28(13):1795-6. doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
Harris EY1, Ponts N, Le Roch KG, Lonardi S.

Marttinen, Pekka, Adam Baldwin, William P. Hanage, Chris Dowson, Esh Mahenthiralingam and Corander, Jukka, 2008,
Bayesian Modeling of Recombination Events in Bacterial Populations,
BMC Bioinformatics 9:421.

ARDEN 1.0 – Specificity Control for Read Alignments Using an Artificial Reference

ARDEN 1.0

:: DESCRIPTION

ARDEN (Artificial Reference Driven Estimation of false positives in NGS data) is a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve.

::DEVELOPER

Bernhard Y. Renard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • HTSeq
  • matplotlib

:: DOWNLOAD

 ARDEN 

:: MORE INFORMATION

Citation

SH Giese, F Zickmann, BY Renard (2014).
Specificity Control for Read Alignments Using an Artificial Reference Genome Guided False Discovery Rate.
Bioinformatics, 2014, 30(1): 9-16 [10.1093/bioinformatics/btt255

LTR_STRUC – LTR Retrotransposon Structure program

LTR_STRUC

:: DESCRIPTION

LTR_STRUC is a new data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Contact with Vinay Mittal ( vinaykmittal@gatech.edu )

:: MORE INFORMATION

Citation:

McCarthy, E.M., and J.F. McDonald. 2003.
LTR_STRUC: A novel search and identification program for LTR retrotransposons.
Bioinformatics 19: 362-367

MESA – MOSLA Error Simulator

MESA

:: DESCRIPTION

MESA is a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms.

::DEVELOPER

Distributed Systems and Intelligent Computing

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MESA

:: MORE INFORMATION

Citation

Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors.
Bioinformatics. 2020 Jun 1;36(11):3322-3326. doi: 10.1093/bioinformatics/btaa140. PMID: 32129840; PMCID: PMC7267826.

MITSU 1.0 – Stochastic EM for Transcription Factor Binding Site Motif Discovery

MITSU 1.0

:: DESCRIPTION

MITSU (Motif discovery by ITerative Sampling and Updating) is a command line application for the discovery of transcription factor binding site (TFBS) motifs.

::DEVELOPER

Alastair M Kilpatrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Java
  • BioJava

:: DOWNLOAD

 MITSU

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i310-i318. doi: 10.1093/bioinformatics/btu286.
Stochastic EM-based TFBS motif discovery with MITSU.
Kilpatrick AM, Ward B, Aitken S.

ASCIIGenome v1.16.0 – Text Only Genome Viewer

ASCIIGenome v1.16.0

:: DESCRIPTION

ASCIIGenome is a command-line genome browser running from terminal window and solely based on ASCII characters.

::DEVELOPER

Dario Beraldi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ASCIIGenome

:: MORE INFORMATION

Citation

Beraldi D.
ASCIIGenome: a command line genome browser for console terminals.
Bioinformatics. 2017 May 15;33(10):1568-1569. doi: 10.1093/bioinformatics/btx007. PMID: 28119307; PMCID: PMC5423454.

SOPanG v2.0.0 – Online Text Searching over a Pan-genome

SOPanG v2.0.0

:: DESCRIPTION

SOPanG (Shift-Or for Pan-Genome) is a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

::DEVELOPER

SOPanG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SOPanG

:: MORE INFORMATION

Citation

Cislak A, Grabowski S, Holub J.
SOPanG: online text searching over a pan-genome.
Bioinformatics. 2018 Dec 15;34(24):4290-4292. doi: 10.1093/bioinformatics/bty506. PMID: 29939210.

CRAMER – Cranfield Genome Browser

CRAMER

:: DESCRIPTION

CRAMER is a customisable, JavaScript and Jade based genome browser for interactive exploration of genomic data. Data is visualized in the browser, meaning CRAMER can be installed on any website and show data from a wide range of online, ftp links or local sources. CRAMER works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3, BAM or delimited text files, and can be customised to parse and display any data source as required.

::DEVELOPER

Mohareb’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java

:: DOWNLOAD

CRAMER

:: MORE INFORMATION

Citation

Anastasiadi M, Bragin E, Biojoux P, Ahamed A, Burgin J, de Castro Cogle K, Llaneza-Lago S, Muvunyi R, Scislak M, Aktan I, Molitor C, Kurowski T, Mohareb F.
CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.
Bioinformatics. 2020 Jun 1;36(11):3556-3557. doi: 10.1093/bioinformatics/btaa146. PMID: 32108858.