Tag: Pipeline

SAAP-BS 1.0 – Streamlined Analysis and Annotation Pipeline for RRBS

SAAP-BS 1.0

:: DESCRIPTION

SAAP-BS (or  SAAP-RRBS) Streamlined Analysis and Annotation Pipeline for Reduced Representation Bisulfite Sequencing) offers an end-to-end solution for analyzing and interpreting next-generation methylation sequencing data. The software integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting, and visualization. With this package, bioinformaticians or investigators can start from sequencing reads and get a fully annotated CpG methylation report quickly allowing more time for biological interpretation.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java
  • Python

:: DOWNLOAD

  SAAP-RRBS

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2180-1. Epub 2012 Jun 10.
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP.

PolyMarker – Fast Polyploid Primer Design Pipeline

PolyMarker

:: DESCRIPTION

PolyMarker is a tool that simplifies the design of genetic markers, a laboratory test to know if certain variant of the genome is present or not in a plant.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069.

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.

FunFrame 0.9.3 – Functional Gene Ecological Analysis Pipeline

FunFrame 0.9.3

:: DESCRIPTION

FunFrame is a pipeline for the ecological analysis of protein-coding genes using targeted metagemomic DNA sequencing. Briefly, FunFrame reads targeted metagenomic sequence data from multiple biological samples, identifies and repairs likely homopolymer read errors, performs ecological analysis on the de-noised sequences, and produces reports describing the microbial communities at each biological sample. The input metagenomic sequence data is typically the product of PCR amplification using universal primers for a specific protein-coding gene prefixed with adaptor and barcode extensions, and read with next-generation pyrosequencing technology.

::DEVELOPER

Jennifer L Bowen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package
  • Python

:: DOWNLOAD

 FunFrame

:: MORE INFORMATION

Citation

FunFrame: functional gene ecological analysis pipeline
David Weisman, Michie Yasuda and Jennifer L. Bowen
Bioinformatics (2013) 29 (9): 1212-1214.

paper-ng-sam – Pipeline for simulating NG-SAM experiments

paper-ng-sam

:: DESCRIPTION

paper-ng-sam is a pipeline for simulating NG-SAM experiments

::DEVELOPER

Botond Sipos

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • r package
  • biopython

:: DOWNLOAD

 paper-ng-sam

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham, Adrian M. Stütz, Nick Goldman (2012)
An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and Next Generation Sequencing.
PLoS ONE 7(8):e43359 doi:10.1371/journal.pone.0043359.

EGene 1.0 – Automated Pipeline Generation System for Sequence Analysis

EGene 1.0

:: DESCRIPTION

EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required.

Coed is a visual tool to facilitate pipeline construction and documentation.

::DEVELOPER

EGene Team

:: SCREENSHOTS

EGene

:: REQUIREMENTS

  • Linux
  • Java
  • Perl
  • PostgreSQL

:: DOWNLOAD

  EGene , Coed

:: MORE INFORMATION

Citation:

Durham, A.M.; Kashiwabara, A.Y.; Matsunaga, F.T.; Ahagon, P.H.; Rainone, F.; Varuzza, L. & Gruber A. (2005).
EGene: a configurable pipeline generation system for automated sequence analysis. 
Bioinformatics 21(12): 2812-2813.

HTPheno – Image Analysis Pipeline for High-Throughput Phenotyping

HTPheno

:: DESCRIPTION

HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.

::DEVELOPER

HTPheno Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 HTPheno

:: MORE INFORMATION

Citation

A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein and F. Schreiber.
HTPheno: An Image Analysis Pipeline for High-Throughput Plant Phenotyping.
BMC Bioinformatics, 12:e148, 2011.

MPP 2.0 – Microarray-to-Phylogeny Pipeline

MPP 2.0

:: DESCRIPTION

MPP (Microarray-to-Phylogeny-Pipeline) is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposonbased insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MPP

:: MORE INFORMATION

Citation:

Davey RP, Savva G, Dicks J and Roberts IN (2007)
MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets.
Bioinformatics 23 (8): 1023-1025

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