Welcome to Satsuma!
Highly sensitive whole-genome synteny alignments.
version 3.1.0
Satsuma is a whole-genome synteny alignment program. It takes two
genomes, computes alignments, and then keeps only the parts that are
orthologous, i.e. following the conserved order and orientation of
features, such as protein coding genes, non-coding genes, or neutral
sequences. Satsuma does not require any pre-processing, such as
repeat masking, since it will automatically detect ambiguous
mappings.
Satsuma has parallelization built-in and is designed to run on
multi-core architectures. The run-time for aligning two bird-size
genomes (~1.2 Gb) is around two days on 24 CPUs.
You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad
Institute's web site.
An incomplete list of questions and answers (yes, these have really
been asked by our users! Please feel free to add your own by
e-mailing us) is here.
If you use Satsuma in your research, please cite:
Grabherr,
M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma,
F., & Lindblad-Toh, K. (2010). Genome-wide synteny through
highly sensitive sequence alignment: Satsuma. Bioinformatics,
26(9), 1145-51.
Recent additions and developments
NEW: the Chromosembler!
Map your scaffolds or contigs onto chromosome coordinates via
synteny! To do so, run
./Chromosemble -t <reference> -q <your_scaffolds> -o
<output_dir>
The full list of options is:
-t<string> : target fasta file (in chromosome coordinates)
-q<string> : query fasta file (the assembly)
-o<string> : output directory
-n<int> : number of CPUs (for full Satsuma run)
(def=25)
-thorough<bool> : runs a full Satsuma alignment
(slow!!) (def=0)
-pseudochr<bool> : maps scaffolds into chromosomes
(def=0)
-s<bool> : run SatsumaSynteny at the end (def=0)
By chromosembling your assembly, you will assign putative chromosome
coordinates to your sequences, while preserving re-arrangements to
the degree possible. Publication and more details coming soon.
Production-quality chromosome figures in pretty colors: we
added a tool, ./ChromosomePaint, to generate chromosomes painted by
synteny. This is what one example based on two fish species looks
like (in low resolution):
Universal Genomic Coordinate Translator: to exploit the power
of synteny to resolve orthologous genes and transcripts, check out
our software Kraken,
which allows to map GTF files across genomes without requiring
all-to-all synteny maps.
Improve the connectivity of your assembly through synteny:
the recently added - and still very experimental - tool
./MergeScaffoldsBySynteny allows for mapping scaffolds onto a
reference genome, while preserving inter- and intrachromosomal
rearrangements. In preliminary tests, we could increase the N50 of
contiguous sequences ('superscaffolds') by up to orders of
magnitudes for NGS based genome assemblies.
Population genomics: if you are interested in finding regions
under specific selective forces within or across populations, you
might find a solution in another software package that we developed,
Saguaro.
(c) 2010, 2014 by Manfred Grabherr, Science for Life Laboratory,
Department of Medical
Biochemistry and Microbiology, Uppsala
University, Uppsala, Sweden, in association with the Broad Institute,
Cambridge, MA, USA.
For more information on the development group, see here.