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SGA specifications

Information


Unique identifier OMICS_00028
Name SGA
Alternative name String Graph Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.10.15
Stability Stable
Maintained Yes

Subtool


  • SGA-preqc

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Jared Simpson

Additional information


https://github.com/jts/sga/wiki/FAQ

Publications for String Graph Assembler

SGA citations

 (22)
library_books

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities

2018
Appl Plant Sci
PMCID: 5895191
PMID: 29732264
DOI: 10.1002/aps3.1034

[…] l., ) builds an ordered k‐mer hash table in Jellyfish 1.x (Marçais and Kingsford, ).The same preprocessing steps and postanalysis filtering were performed in all analyses. The genome assembly program String Graph Assembler (Simpson and Durbin, ; Simpson, ) was used to clean raw read data to remove duplicate, repetitive, and low‐quality reads (for details, see: https://github.com/rsh249/ISOETES1/bl […]

call_split

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

2018
Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w
call_split See protocol

[…] ra/).B. floridae, H. sapiens: Joint Genome Institute (JGI, http://genome.jgi.doe.gov).Quality assessment comparison data for Homo sapiens, Maylandia zebra, Melopsittacus undulatus, Crassostrea gigas: String Graph Assembler (https://github.com/jts/sga/tree/master/src/examples/preqc).The data of the B. leachii genome is available from the following sources:Raw sequence reads: National Center for Bio […]

call_split

Routine Whole Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

2018
Front Microbiol
PMCID: 5869177
PMID: 29616014
DOI: 10.3389/fmicb.2018.00511
call_split See protocol

[…] cing adapters using Trimmomatic (). Then, the reads were filtered and trimmed further according to quality and length criteria (Supplementary Table ) using Trimmomatic and the pre-process function of String Graph Assembler SGA (Supplementary Table ) (). Finally, SGA was used to correct errors in the reads by a k-mer frequency-based method. After being quality filtered and error corrected, the read […]

call_split

Genome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207

2018
Sci Rep
PMCID: 5827749
PMID: 29483539
DOI: 10.1038/s41598-018-21919-4
call_split See protocol

[…] er with 2 × 300 bp pair-end library. A total of 794,028 reads (55× coverage of the genome) were generated, cleaned and quality filtered using Trimmomatic. Reads were then corrected for errors through String graph assembler which utilizes a k-mer centric algorithm. De novo assembly was attempted through IDBA-UD algorithm centred on de bruijn graph approach. Genome annotation was carried out using t […]

library_books

A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective

2018
Evol Bioinform Online
PMCID: 5826002
PMID: 29511353
DOI: 10.1177/1176934318758650

[…] west memory on both prokaryotic paired-end and single-end data sets; Velvet and Edena consumed lowest memory on eukaryotic single-end data sets; and SSAKE on eukaryotic paired-end data sets. SGA, the string graph assembler, was also a good choice to assemble paired-end data sets consuming low memory, but in terms of assembler data transformation, SGA consumed more time in indexing, correction, dup […]

library_books

Phylogeny and putative virulence gene analysis of Bartonella bovis

2017
PMCID: 5938196
PMID: 29311425
DOI: 10.1292/jvms.17-0448

[…] na platform with 100 bp paired-end reads. The reads were then subjected to adapters and low quality reads trimming based on Q25 using Trimmomatics [] and Sycthe (https://github.com/vsbuffalo/scythe). String Graph Assembler (SGA) [] was used for error correction. After pre-analysis, the reads were subjected to de novo genome assembly, using IDBA-UD, a de novo assembler for sequencing data with high […]

Citations

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SGA institution(s)
Ontario Institute for Cancer Research, Toronto, ON, Canada
SGA funding source(s)
Supported by the Wellcome Trust Sanger Institute (Wellcome Trust grant 098051) and by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario.

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