Software
Basic Tools
Notes:
UnFastaFormat: Convert fasta files into tab-delimited format. Includes a quality score safe option (-q)
for converting quality score files.
Download: UnFastaFormat.exe, UnFastaFormat.pl
UnFastQFormat: Convert fastq files into tab-delimited format. Outputs sequences and quality scores
into separate files. Edits sequence titles. Support for NCBI and Illumina formats.
v1.2. bug fixes and generic title parsing
Download: UnFastQFormat.exe, UnFastQFormat.pl
FastaFormat: Convert tab-delimited files into fasta format. Includes a quality score safe option (-q) for
converting quality score files.
Download: FastaFormat.exe, FastaFormat.pl
QuickSort: Sort tab-delimited text rows by specific columns, with or without replacement.
Download: QuickSort.exe, QuickSort.pl
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
>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 (e.g. C:>script1.exe -h) for a
general description of function followed by option list.
>Contact author for bugs, comments, or questions: jcv128@psu.edu
