Cpipe 2.5.1 – Exome Sequencing Pipeline

Cpipe 2.5.1

:: DESCRIPTION

Cpipe is a variant detection pipeline designed to process high throughput sequencing data (sometimes called “next generation sequencing” data), with the purpose of identifying potentially pathogenic mutations.

::DEVELOPER

the Melbourne Genomics Health Alliance

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Cpipe

:: MORE INFORMATION

Citation:

Cpipe: a shared variant detection pipeline designed for diagnostic settings.
Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.
Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x.

CG-Pipeline 0.4.4- Computational Genomics Pipeline

CG-Pipeline 0.4.4

:: DESCRIPTION

CG-Pipeline is an analytical pipeline for the analysis of prokaryotic genome sequences. Includes genome assembly, gene prediction and fucntional annotation.

::DEVELOPER

Jordan Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • BioPerl

:: DOWNLOAD

 CG-Pipeline

:: MORE INFORMATION

Citation

Kislyuk, A. O., L. S. Katz, S. Agrawal, M. S. Hagen, A. B. Conley, P. Jayaraman, V. Nelakuditi, J. C. Humphrey, S. A. Sammons, D. Govil, R. D. Mair, K. M. Tatti, M. L. Tondella, B. H. Harcourt, L. W. Mayer, and I. K. Jordan. 2010.
A computational genomics pipeline for prokaryotic sequencing projects.
Bioinformatics 26:1819-26.

Parallel-META 3.2.0 – A Parallel Metagenomic Analysis Pipeline

Parallel-META 3.2.0

:: DESCRIPTION

Parallel-META is a GPGPU and Multi-Core CPU based software which can parallelly analyze massive metagenomic data structures, report the classification, construction and distribution on phylogenetic & taxonomic and functional level.

::DEVELOPER

Computational Biology Group, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • R

:: DOWNLOAD

 Parallel-META

:: MORE INFORMATION

Citation

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.
Su X, Pan W, Song B, Xu J, Ning K.
PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.
Su X, Xu J, Ning K.
BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16.

piPipes 1.4.12 – piRNA Pipeline Collection

piPipes 1.4.12

:: DESCRIPTION

piPipes is a coordinated set of pipelines to analyze piRNA (PIWI-interacting RNAs) and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq.

::DEVELOPER

the Zamore Lab and ZLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • C++ Compiler

:: DOWNLOAD

 piPipes

:: MORE INFORMATION

Citation

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
Han BW, Wang W, Zamore PD, Weng Z.
Bioinformatics. 2014 Oct 17. pii: btu647.

GWASpi 2.0.2 – Genome Wide Association Study pipeline

GWASpi 2.0.2

:: DESCRIPTION

GWASpi is a start-to-finish GWAS management application that uses a novel approach on database technologies to reduce in up to two orders of magnitude the time needed to perform the fundamental steps of a GWAS. GWAS  based on Single Nucleotide Polymorphism (SNP) arrays are the most widely used approach to detect loci associated to human traits. Due to the complexity of the methods and software packages available, each with its particular format requiring intricate management work-flows, the analysis of GWAS usually confronts scientists with steep learning curves. Indeed, the wide variety of tools makes the parsing and manipulation of data the most time-consuming and error prone part of a study. To help solving these issues, we present GWASpi, a user-friendly, multi-platform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware. GWASpi is a start-to-finish GWAS management application, from raw data to results, containing the most common analysis tools. As a result, GWASpi is easy to use and reduces in up to two orders of magnitude the time needed to perform the fundamental steps of a GWAS.

::DEVELOPER

Evolutionary Genomics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 GWASpi

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 1;27(13):1871-2. Epub 2011 May 17.
Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management.
Muñiz-Fernandez F, Carreño-Torres A, Morcillo-Suarez C, Navarro A.

AffyPipe – Pipeline for Affymetrix Axiom Genotyping Workflow

AffyPipe

:: DESCRIPTION

AffyPipe allows you to edit SNP probe classes directly while exporting genotypes in PLINK format

::DEVELOPER

AffyPipe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Python

:: DOWNLOAD

 AffyPipe

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 1;30(21):3118-9. doi: 10.1093/bioinformatics/btu486.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.
Nicolazzi EL, Iamartino D, Williams JL

DAWGPAWS 1.1 – Genome Annotation Pipeline

DAWGPAWS 1.1

:: DESCRIPTION

DAWGPAWS (Distributed Annotation Working Group approach for a Pipeline to Annotate Wheat Sequences) is a tool for discovering the location of the genes and transposable elements in eukaryotic genomic sequences. It is distributed as a suite of command line programs that are designed to assist a Distributed Annotation Working Group (DAWG) in the annotation of genomic sequence contigs.

::DEVELOPER

James C. Estill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Perl
  • Bioperl

:: DOWNLOAD

  DAWGPAWS

:: MORE INFORMATION

Citation

JC Estill and JL Bennetzen. 2009.
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.”
Plant Methods. 5:8.

gNOME – Whole Genome Sequencing Analysis Pipeline

gNOME

:: DESCRIPTION

gNOME is an interactive whole-genome analysis pipeline to prioritize disease-linked variants, genes, and pathways

::DEVELOPER

gNOME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hum Mutat. 2014 May;35(5):537-47. doi: 10.1002/humu.22520. Epub 2014 Mar 6.
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline.
Lee IH1, Lee K, Hsing M, Choe Y, Park JH, Kim SH, Bohn JM, Neu MB, Hwang KB, Green RC, Kohane IS, Kong SW.