IM-TORNADO 2.0.3.2 – Illinois Mayo Taxonomy Operations for RNA Database Operations

IM-TORNADO 2.0.3.2

:: DESCRIPTION

IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.

::DEVELOPER

IM-TORNADO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IM-TORNADO

:: MORE INFORMATION

Citation

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries.
Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N.
PLoS One. 2014 Dec 15;9(12):e114804. doi: 10.1371/journal.pone.0114804. eCollection 2014.

SeqToolBox 0.02 – A set of Perl modules and scripts for Operations on Sequence data

SeqToolBox 0.02

:: DESCRIPTION

SeqToolBox is a set of Perl modules and scripts for day to day operations on sequence data. Includes, parsers for standard file formats and some utility modules, such as modules for working with “sets”, a set of modules for handling NCBI taxonomy database etc. The bin directory contains some scripts to run jobs on clusters.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  SeqToolBox

:: MORE INFORMATION

GROK 1.1.1 – Genomic Region Operation Toolkit

GROK 1.1.1

:: DESCRIPTION

GROK is “Swiss Army knife” library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

 GROK

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):200-6. doi: 10.1109/TCBB.2012.170.
Genomic region operation kit for flexible processing of deep sequencing data.
Ovaska K1, Lyly L, Sahu B, J?nne OA, Hautaniemi S.

MISO 0.2.195 – Managing Information for Sequencing Operations

MISO 0.2.195

:: DESCRIPTION

MISO is a new open-source Lab Information Management System (LIMS) under development at TGAC, specifically designed for tracking next-generation sequencing experiments.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MISO

:: MORE INFORMATION

bamUTIL 1.0.14 – Perform Operations on SAM/BAM files

bamUTIL 1.0.14

:: DESCRIPTION

bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 bamUTIL

:: MORE INFORMATION