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Satsuma specifications

Information


Unique identifier OMICS_03700
Name Satsuma
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Manfred Grabherr

Publication for Satsuma

Satsuma citations

 (17)
library_books

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

2018
Mol Biol Evol
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] ted using only the autosomal chromosomes in PSMC (). Scaffolds representing the X chromosome of the striped hyena were determined through a synteny analysis to the cat X chromosome (CM001396.2) using Satsuma synteny (). These scaffolds were then removed along with any scaffold shorter than 1 Mb. A consensus diploid sequence was constructed using Samtools (Li et al. 2009) to be used as input for PS […]

library_books

Inferring synteny between genome assemblies: a systematic evaluation

2018
BMC Bioinformatics
PMCID: 5791376
PMID: 29382321
DOI: 10.1186/s12859-018-2026-4

[…] The four anchor-based programs DAGchainer [], i-ADHoRe [] (v3.0), MCScanX [] and SynChro [], and the nucleotide alignment-based Satsuma [], were used to identify synteny blocks. Settings for each program were modified to resemble each other on the results of C. elegans vs. C. elegans, where synteny should be close to 100%, wit […]

library_books

Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration

2017
Nat Commun
PMCID: 5741667
PMID: 29273779
DOI: 10.1038/s41467-017-01964-9

[…] set of 428 consensus repeat sequences larger than 1000 nt. Out of these, 349 were identified as known repeats through nucleotide alignments against RepBase (version 21.10 downloaded 10/23/2016) using Satsuma (https://sourceforge.net/projects/satsuma/ last update 2016-12-14) and selecting the longest alignments respectively if multiple overlapping hits were reported. […]

library_books

The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages

2017
Sci Rep
PMCID: 5648845
PMID: 29051555
DOI: 10.1038/s41598-017-13911-1

[…] e International Committee on the Taxonomy of Viruses (ICTV), the nucleotide similarity between phages of the same genus should be more than 50%. Using a highly sensitive nucleotide alignment program, Satsuma, only 15–21% of the total genome could be aligned to the closest references and with an average similarity of 50%. No significant nucleotide similarities was found with BLASTN. The combination […]

library_books

Evaluation of single cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

2017
Sci Rep
PMCID: 5591225
PMID: 28887541
DOI: 10.1038/s41598-017-11466-9

[…] t possible local rearrangements between our SAGs and the M. brevicollis MX1 strain, we aligned the non-contaminant scaffolds of the pooled assembly (query) against the reference genome (target) using Satsuma v3.1.0a with default parameters. We then used the SatsumaSynteny module to compute whole-genome synteny blocks, which were manually examined to identify cases of genomic rearrangements. Specif […]

library_books

The house spider genome reveals an ancient whole genome duplication during arachnid evolution

2017
BMC Biol
PMCID: 5535294
PMID: 28756775
DOI: 10.1186/s12915-017-0399-x

[…] ded signals of synteny such as signatures of ancient WGDs that were followed by numerous rearrangements. For visualization, we selected only the 100 scaffolds for which the number of hits detected by Satsuma was maximal; in a second round, this list was further reduced to the set of 39 scaffolds that exhibited the greatest number of hits with each other. An Oxford grid [] was drawn using the tool […]

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Satsuma institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Satsuma funding source(s)
Supported by National Human Genome Research Institute (Large Scale Sequencing and Analysis of Genomes, grant no. NIH 1 U54 HG03067, Lander) and ESF EURYI award recipient.

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