Site Identification from Short Read Sequences.
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SISRS: Site Identification from Short Read Sequences
Version 1.6
Copyright (c) 2013-2016 Rachel Schwartz
More information: Schwartz, R.S., K.M Harkins, A.C. Stone, and R.A. Cartwright. 2015. A composite genome approach to identify phylogenetically informative data from next-generation sequencing. BMC Bioinformatics. 16:193. (

Talk from Evolution 2014 describing SISRS and its application:


This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.



Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.

Running SISRS


sisrs command options

By default, SISRS assumes that

  • A reference genome is not available.
  • The K-mer size to be used by Velvet in contig assembly is 21.
  • Only one processor is available.
  • Files are in fastq format.
  • A site is only required to have data for two species to be included in the final alignment.
  • Folders containing reads are in the present working directory.
  • A minimum of three reads are required to call the base at a site for a taxon.


  • sites : produce an alignment of sites from raw reads
  • alignContigs : run sisrs skipping the composite genome assembly
  • mapContigs : run sisrs, also skipping alignment of reads to composite genome
  • identifyFixedSites : run sisrs, also skipping mapping of contigs to a reference
  • outputAlignment : get sisrs alignment from sites id'd for individual species
  • loci : produce a set of aligned loci based on the most variable regions of the composite genome


  • -g : MANDATORY if running sisrs from the beginning - the approximate genome size
    • this will reduce the size of the composite assembly by using a subset of reads to approximate 10x coverage
  • -p : use this number of processors
  • -r : the path to the reference genome in fasta format
  • -k : k-mer size (for assembly)
  • -f : the folder containing the folders of reads
  • -n : the number of reads required to call a base at a site
  • -t : the threshold for calling a site; e.g. 0.99 means that >99% of bases for that taxon must be one allele; only recommended for low ploidy with <3 individuals
  • -m : the number of species that are allowed to have missing data at a site
  • -o : the length of the final loci dataset for dating
  • -l : the number of alleles for sisrs loci
  • -a : assembler (velvet, minia, or abyss)


Nexus file with variable sites in a single alignment. Usable in most major phylogenetics software as a concatenated alignment with a setting for variable-sites-only.

Test Data

The folder test_data contains simulated data for 10 species on the tree found in simtree.tre . Using 40 processors this run took 9 minutes. Analysis of the alignment output by sisrs using raxml produced the correct tree.

Sample commands

  1. Basic sisrs run: start with fastq files and produce an alignment of variable sites

    sisrs sites -g 1745690

  2. Basic sisrs run with modifications

    sisrs sites -g 1745690 -p 40 -m 4 -f test_data -t .99 -a minia

  3. Produce an alignment of loci based on the most variable loci in your basic sisrs run. Note - this command will run sisrs sites if (and only if) it was not run previously.

    sisrs loci -g 1745690 -p 40 -l 2 -f .

  4. Get loci from your fastq files given known loci.

    first name your reference loci ref_genes.fa and put in your main folder

    sisrs loci -p 40 -f test_data