LmCGST 1.0 – Molecular Characterization with Next-generation Sequence data

LmCGST 1.0

:: DESCRIPTION

LmCGST is a bioinformatic pipeline that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis.

::DEVELOPER

LmCGST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data.
Pightling AW, Petronella N, Pagotto F.
BMC Microbiol. 2015 Oct 22;15(1):224. doi: 10.1186/s12866-015-0526-1.

ComB 2.0.4-1 -Downstream Mapping Analysis for Next Generation Sequence Data

ComB 2.0.4-1

:: DESCRIPTION

ComB is a software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms. ComB operates on the mapping output produced by the mapping program PerM and is capable of providing SNP calls, resequencing output, and expression analysis.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ComB

:: MORE INFORMATION

Citation:

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.
ComB: SNP calling and mapping analysis for color and nucleotide space platforms.
Souaiaia T, Frazier Z, Chen T.

Tablet 1.21.02.08 – Next Generation Sequence Assembly Visualization

Tablet 1.21.02.08

:: DESCRIPTION

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Tablet

:: MORE INFORMATION

Citation

Milne, I, Bayer, M, Cardle, L, Shaw, P, Stephen, G, Wright, F and Marshall, D. 2010.
Tablet – next generation sequence assembly visualization.
Bioinformatics 26(3), 401-402.

Mercury 3.2.1 – Next Generation Sequence Analysis Pipeline

Mercury 3.2.1

:: DESCRIPTION

Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Valence
  • Perl
  • Python

:: DOWNLOAD

Mercury

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 29;15:30. doi: 10.1186/1471-2105-15-30.
Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.
Reid JG1, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E.