POSA - Perl Objects for Sequencing Data Analysis

Paper

For the paper in BMC Genomics describing this tool, see here

Download

For development info and download, see the Sourceforge website.

Reference

When using these objects, please use the following reference: Aerts JA, Jungerius BJ and Groenen MAM. POSA: perl objects for DNA sequencing data analysis. BMCGenomics 5:60 (2004)

Help wanted

It would be great to have a webinterface to select from basic pipelines. Any help appreciated.

Description

Capillary DNA sequencing machines allow to generate vast amounts of data with little hands-on time. With this expansion of data generation, there is also a growing need for automated data processing. Most available software solutions, however, still require user intervention (eg. Staden package) or provide modules that need advanced informatics skills to be implemented in pipelines(eg. bioperl). Here we present Read.pm and Contig.pm – two new perl objects that describe a DNA sequence read and a phrap contig assembly in detail. These objects allow a flexible and easy setup of perl based pipelines including generating primer3 input and automated SNP discovery, while requiring only little programming skills.

Requirements

Perl interpreter v.5.006
Perl modules: Carp; Statistics::Descriptive; Tie::File; IO::File; POSIX Storable.
Phred, Phrap and PolyPhred
Tested under Linux (Suse 8.1)
Staden Package (optional)
Primer3 (optional)

Installation instructions

Detailed instructions for installation are found here.

Features

import sequence reads from abi, scf, exp or fasta formats.
basecalling and quality values (phred)
clipping good quality sequence
vector clipping
export to scf, exp or fasta format
generation of primer3 input file
contig building using gcphrap
export of contigs as alignments
find putative SNPs (PolyPhred)
screen for putative heterozygous SNPs
filter against false-negative or false positive SNPs
...

Downloads:

Download the objects: POSA-0.8.tar.gz (~7 Mb; tar.gz format)
man page of Read.pm
man page of Contig.pm

Examples:

See here.

Contact

We would appreciate it when you would drop us an email. This would help us to keep track of users and their demands and would aid in improving the provided objects.

Jan Aerts
Animal Breeding and Genetics Group
Department of Animal Sciences
Wageningen University
P.O. Box 338
6700 AH Wageningen
The Netherlands
janDOTaertsATwurDOTnl
tel +31 317 483397
fax +31 317 483929