Software
BETAS
Notes:
SNPHunter: Searches an alignment file (e.g. AceParser output) for SNPs using multiple parameters and filters (works with AssemblyFilter) for quality, homopolymer runs, and alternative splicing/assembly error. Options to include Blast annotation and ORF information for codon position and synonomous/nonsynonymous amino acid changes and to generate population specific output.
Download version:
2.22: SNPHunter.exe, AssemblyFilter.exe
2.10: SNPHunter.exe, AssemblyFilter.exe
1.00: SNPHunter1.exe
Doc: SNPHunterOverview
>These perl scripts are designed to be run from the Windows command-prompt (Vista/7) and have standard Unix/DOS-like options functunality.
e.g. C:>script1.exe -i input.txt -o output.txt etc.

>Both pre-packaged executables (exe) and code (pl) are available for most of the scripts. Executables are optimized for 64-bit Windows and may or may not function on 32-bit systems.

>All scripts include a help option for a general description of function followed by option list.
e.g. C:>script1.exe -h

>Feel free to contact me
for bugs or suggestions at: jcv128@psu.edu

AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.
Download version:
1.33: AceParser.exe
1.31: AceParser.exe
TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.50 includes simple sequencing error model and slightly more realistic 454 error model. Version 0.70 has simulated SNPs/Indels with an improved model.
Download version:
0.70: TranscriptSimulator.exe, TranscriptSimulatorNotes.txt
QualSim: Very experimental text-based Phred quality score simulator for next-gen sequencer output. Intended for use with TranscriptSimulator script. Attempts to create realistic quality scores for a gene sequence set using a large amount of training data (e.g. 454 reads).
Download version:
0.40: QualSim.exe
SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their nucleotide templates using read title inforamation, creating ideal simulated assembly of super contigs.
Download version:
0.20: SimAssemblyStage1.exe
SimAssemblyStage2: Creates an optimal simulated assembly alignment of contigs using the output of SimAssemblyStage1.
Download version:
0.20: SimAssemblyStage2.exe
TableParser: Simple tool for extracting sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parses out contigs, singletons, and assembled reads into separate files.
Download: TableParser.exe, TableParser.pl