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
2.22: SNPHunter.exe, AssemblyFilter.exe
2.10: SNPHunter.exe, AssemblyFilter.exe
>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
e.g. C:>script1.exe -h
>Feel free to contact me
for bugs or suggestions at: firstname.lastname@example.org
AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited
assembly alignment file. Options to include embedded annotation from
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.
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).
SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their
nucleotide templates using read title inforamation, creating ideal simulated
assembly of super contigs.
SimAssemblyStage2: Creates an optimal simulated assembly alignment of
contigs using the output of SimAssemblyStage1.
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