Satsuma protocols

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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

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Maintainer


  • person_outline Manfred Grabherr <>

Publication for Satsuma

Satsuma in pipeline

2016
PMCID: 4833346
PMID: 27082250
DOI: 10.1371/journal.pgen.1005954

[…] chromosome scale assembly (v3) of l. calcarifer with d. labrax and g.aculeatus genomes were performed by last [] and filtered by single_cov2. maf output files were subsequently converted to the satsuma format by custom scripts (awk) and processed by the blockdisplaysatsuma script from the satsuma v1.17 package [] to result in coordinates of syntenic blocks between the different genomes. […]


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Satsuma in publications

 (13)
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] in our assembly likely to originate from the x chromosome before running demographic analyses. we aligned our striped hyena assembly by synteny () to the cat x chromosome (126,427,096 bp) using satsuma () and found 195 scaffolds (, online), totaling 117,479,157 bp. the alignments were visualized using circos () (, online). the circos alignment showed that the scaffolds found using satsuma […]

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

[…] 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., we computed pairwise genomic […]

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

[…] number nc_019408.1], which were determined to be the closest related sequences by blastn. comparisons were made on an amino acid level between genomes using tblastx and on a nucleotide level with satsuma for increased sensitivity when comparing sequences with little similarity. tblastx hits were filtered for a minimum of 50% identity over a minimum of 50 amino acids, while satsuma options […]

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

[…] 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. […]

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

[…] 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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