Software
Basic Tools
FastQFormat: Convert tab-delimited sequence and quality score files into fastQ format.
Download: FastQFormat.exe, FastQFormat.pl
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
RemoveRowClones2: Removes duplicate rows in a column of input. Much faster algorithm.
Download: RemoveRowClones2.exe,RemoveRowClones2.pl
CopyColumn: Copy a column from tab-delimited input.
Download: CopyColumn.exe, CopyColumn.pl
ColumnEditor2: Edit a column from tab-delimited input.
Download: ColumnEditor2.exe, ColumnEditor2.pl
CombineStreams: Combine tab-delimited input columns from two sources for piping.
Download: CombineStreams.exe, CombineStreams.pl
RipSelectedRows: Removes rows from tab-delimited input using a list.
Download: RipSelectedRows.exe, RipSelectedRows.pl
RipColumn: Remove a column from tab-delimited input.
Download: RipColumn.exe, RipColumn.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