Summary

XSTK is a suite of C and C++ libraries and command-line programs for DNA sequence analysis.  Tested on Mac OSX and a variety of Linux systems.

Includes source code for the following programs:

barcrawl -- Design of barcoded oligonucleotides for multiplex sequencing.

bartab --  Annotation, binning and dereplication of barcoded DNA sequences.

            --  Now inputs fastq format and allows barcodes on 3’ ends of reads.

biodiv -- Calculation of common ecological biodiversity indices.

sortx -- OTU clustering of aligned sequences.

fa2fq -- Translate from fasta to fastq format.

fq2fa -- Translate from fastq to fasta format.

fa2nw -- Create newick-format selection tree from fasta file.

nm2nw -- Create newick-format selection tree from list of taxon names.

Download

By downloading this software you certify that you will use XSTK solely under the terms outlined in the license agreement.  Click on the link to download.  Once downloaded, double click the tar.gz file to uncompress.   Installation instructions are provided in the INSTALL file of the xstk directory.

      

Citation

For barcrawl and bartab:

Frank DN (2009) BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 10: 362.

All others:  Frank DN (2009) Personal communication.

Contact

Daniel N. Frank, Ph.D.  daniel(dot)frank at ucdenver(dot)edu

Copyright 1999-2010

XplorSeq ToolKit

Tools for nucleic acids sequence analysis

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