GAA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GAA
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Tool usage distribution map

This map represents all the scientific publications referring to GAA per scientific context
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GAA specifications

Information


Unique identifier OMICS_09319
Name GAA
Alternative name Graph Accordance Assembly
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Graph Accordance Assembly

GAA citations

 (4)
library_books

The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

2018
BMC Genomics
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] nd within these contigs 650 Mbp was assembled. JR-assembler assembled 370,267 contigs (> 500 bp) with an N50 of 1.3 kbp and a total assembled length of 433 Mbp. After merging the two assembles with a graph accordance assembly program [], the A. limnaeus draft genome assembly v1.0 has 168,369 contigs, has a contig N50 of 8.1 kb, and is 695 Mbp in total length. Use of mate-pair libraries for scaffol […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] rence genome as a template. MAIA was implemented on top of the Matlab programming language and is available as a package for it that can be obtained from the URL http://bioinformatics.tudelft.nl.GAA (Graph Accordance Assembly) (): is an assembly integration software that is based on a homonymous data structure. Taking a set of contigs as input, the tool uses BLAT () to generate alignments, identif […]

library_books

IMA Genome F 6

2016
PMCID: 4941685
PMID: 27433447
DOI: 10.5598/imafungus.2016.07.01.11

[…] assessing single-copy orthologs with BUSCO (). Based on these metrics, the best assemblies from the corrected PacBio and Illumina read datasets were chosen to create an improved hybrid assembly using Graph Accordance Assembly program (GAA) (). Scaffolds were generated with SSpace (). Gene predication utilized RepeatMasker v. 0.10.1 (described in ) to remove repeat and low complexity DNA regions fo […]

library_books

Chromosomal Transfers in Mycoplasmas: When Minimal Genomes Go Mobile

2014
MBio
PMCID: 4251992
PMID: 25425234
DOI: 10.1128/mBio.01958-14

[…] of the transconjugant M69-71 was achieved using Illumina sequencing (MiSeq; mating pair libraries). De novo assembly was done using ABySS () and CLC (Qiagen) software before assembly fusion with GAA (graph accordance assembly, version 1.1) () and a further scaffolding and in silico finishing using OPERA (version 1.4) () and the position information deduced from the mating pair sequencing. […]


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GAA institution(s)
The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
GAA funding source(s)
National Human Genome Research Institute (grant HG004968)

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