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 barcoded oligonucleotides for multiplex sequencing.
bartab -- Annotate, bin and dereplicate barcoded DNA sequences.
biodiv -- Calculation of common ecological biodiversity indices.
minerna -- Extract rRNA sequences from GenBank file.
sortx -- OTU clustering of aligned sequences.
xscat -- Merge sequences in two fasta/q files.
xschim -- Create chimeric sequences.
xscrossout -- Post-process cross_match output.
xsdegap -- Remove gaps from fasta/q alignment file.
xsdstcmp -- Calculate distance matrix between two alignments. Infers
taxonomy of query sequences from nearest match in first alignment.
xsel -- Select sequences from fasta/q file (use xsub to select subsequences).
xsqualgap -- Align quality scores with sequences in fasta format.
xsrep -- Dereplicate sequences in fasta/q file.
xsstat -- Collect basic statistics for sequences in fasta/q file.
xstrim -- Trim DNA sequences based on quality scores.
xsub -- Extract sub-alignment from multiple sequence alignment (fasta format).
Parsers:
fa2fq -- Translate from fasta to fastq format.
fa2nm -- List deflines in fasta file.
fa2nw -- Create newick-format selection tree from fasta file.
fa2qu -- Construct mock quality score file for fasta file.
fa2sto -- Translate from fasta to Stockholm format.
fq2fa -- Translate from fastq to fasta format.
gb2fa -- Translate from GenBank to fasta format.
nm2nw -- Create newick-format selection tree from list of taxon names.
si2fa -- Translate from SINA to fasta format.
sto2fa -- Translate from Stockholm to fasta format.
