SRCP 1.0 – Sequence Read Classification Pipeline

SRCP 1.0

:: DESCRIPTION

The SRCP is a high-throughput, automated data analysis pipeline that is used to classify genomic shotgun reads into functional/descriptive sequence categories. It represents a powerful means of rapidly describing the sequence content of a genome and a standardized method for estimating gene/repeat enrichment or reduction afforded by Cot filtration, CBCS, and/or other reduced-representation sequencing (RRS) techniques

:: DEVELOPER

the Institute for Genomics, Biocomputing & Biotechnology (IGBB).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Perl

:: DOWNLOAD

SRCP

:: MORE INFORMATION

Citation

Anal Biochem. 2008 Feb 1;373(1):78-87.
An automated, high-throughput sequence read classification pipeline for preliminary genome characterization.
Chouvarine P, Saha S, Peterson DG.

HapCUT2 v1.3.1 – Haplotype Assembly or Haplotype Phasing using Sequence Reads from a Diploid Genome

HapCUT2 v1.3.1

:: DESCRIPTION

HapCUT is a max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. It can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants (VCF file), and outputs the phased haplotype blocks that can be assembled from the sequence reads.

::DEVELOPER

Vikas Bansal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX

:: DOWNLOAD

HapCUT

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 15;24(16):i153-9. doi: 10.1093/bioinformatics/btn298.
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.
Bansal V, Bafna V.

AgileSamFileSorter 20120105 – Ordering Sequence Reads in a *.sam file by Chromosome and Map Position

AgileSamFileSorter 20120105

:: DESCRIPTION

AgileSAMFileSorter reads the sequence reads in an unsorted *.sam file and creates a second *.sam file in which all the sequence reads are sorted by chromosome number and position.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft .NET framework version 2.0

:: DOWNLOAD

AgileSamFileSorter

:: MORE INFORMATION

TASR 1.6.2 – Targeted Assembly of Sequence Reads

TASR 1.6

:: DESCRIPTION

TASR (Targeted Assembly of Sequence Reads) is a genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Perl

:: DOWNLOAD

TASR

:: MORE INFORMATION

Citation

Warren RL, Holt RA.
Targeted assembly of short sequence reads.
PLoS One. 2011 May 11;6(5):e19816.

GPSeq 0.5 – Using the Generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

GPSeq 0.5

:: DESCRIPTION

GPSeq is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows
R package/Perl/C Compiler

:: DOWNLOAD

GPSeq

:: MORE INFORMATION

Citation:

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670.

WMap 20091230 – Mapping of Sequence Reads

WMap 20091230

:: DESCRIPTION

WMap is a new sequence mapping software designed to map high-throughput sequencing reads as well as methylated-C reads, enabling usage of such sequencing data to various fields of biological research.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux
Java

:: DOWNLOAD

WMap

:: MORE INFORMATION

seq2HLA 2.3 – HLA typing from RNA-Seq sequence reads

seq2HLA 2.3

:: DESCRIPTION

seq2HLA is a software for obtaining an individual’s human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
Python / R package

:: DOWNLOAD

seq2HLA

:: MORE INFORMATION

Citation

Genome Med. 2013 Dec 22;4(12):102. [Epub ahead of print]
HLA typing from RNA-Seq sequence reads.
Boegel S, Löwer M, Schäfer M, Bukur T, de Graaf J, Boisguérin V, Türeci O, Diken M, Castle JC, Sahin U.