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Atlas-Link specifications

Information


Unique identifier OMICS_00040
Name Atlas-Link
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Atlas-Link citations

 (15)
library_books

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

2018
Sci Rep
PMCID: 5792627
PMID: 29386578
DOI: 10.1038/s41598-018-20154-1

[…] ALLPATHS-LG v35218 was used to assemble reads. Two approaches were used to scaffold contigs and close gaps in the genome assembly. The reference genome used in downstream analyses was generated with ATLAS-LINK v1.0 and ATLAS GAP-FILL v2.2 (https://www.hgsc.bcm.edu/software/). In the second approach, REDUNDANS was used, as it is optimized to deal with heterozygous samples. The raw sequence data an […]

library_books

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host

2018
Nature
PMCID: 5843367
PMID: 29300007
DOI: 10.1038/nature25140

[…] ting 100-bp paired-end reads. Raw sequences have been deposited in NCBI under Bioproject PRJNA157077. Reads were assembled using ALLPATHS-LG and further scaffolded and gap-filled using in-house tools Atlas-Link (v.1.0) and Atlas GapFill (v.2.2) (https://www.hgsc.bcm.edu/software/). Atlas-link is a scaffolding or super-scaffolding method that uses all unused mate pairs to increase scaffold sizes an […]

library_books

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

2017
BMC Biol
PMCID: 5689209
PMID: 29145861
DOI: 10.1186/s12915-017-0439-6

[…] . Sequencing was performed on Illumina HiSeq 2000 instruments generating 100 bp PE reads. Reads were assembled using ALLPATHS-LG (v35218) [] and further scaffolded and gap-filled using in-house tools Atlas-Link (v.1.0) and Atlas GapFill (v.2.2) (https://www.hgsc.bcm.edu/software/). Atlas-link is a scaffolding or super-scaffolding method that utilizes all unused mate pairs to increase scaffold size […]

call_split

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
call_split See protocol

[…] as described above.Sequencing was performed using Illumina HiSeq2000 generating 100 bp paired-end reads. Reads were assembled using ALLPATHS-LG (v35218) [] and further scaffolded and gap-filled using Atlas-Link (v.1.0) and Atlas gap-fill (v.2.2) []. For P. tepidariorum, this yielded an assembly size of 1443.9 Mb with 263,833 contigs with an N50 of 10.1 kb and, after scaffolding and gap closing, 31 […]

library_books

Evolutionary History of Chemosensory Related Gene Families across the Arthropoda

2017
Mol Biol Evol
PMCID: 5850775
PMID: 28460028
DOI: 10.1093/molbev/msx147

[…] support automated and manual annotation.The genomic sequence of the copepod E. affinis was assembled using ALLPATHS-LG (release 3‐35218) () and further scaffolded and gap-filled using in-house tools Atlas-Link (v.1.0) and Atlas gap-fill (ver.2.2) (https://www.hgsc.bcm.edu/software; last accessed May 4, 2017). This yielded an assembly of size 494.8 Mb including gaps within scaffolds, with contig N […]

library_books

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

2016
Genome Biol
PMCID: 5105290
PMID: 27832824
DOI: 10.1186/s13059-016-1088-8

[…] ctively. Sequencing was performed on Illumina HiSeq2000s generating 100-bp paired-end reads. Reads were assembled using ALLPATHS-LG (v35218) and further scaffolded and gap-filled using in-house tools Atlas-Link (v.1.0) and Atlas gap-fill (v.2.2) (https://www.hgsc.bcm.edu/software/). Data for the A. glabripennis genome have been deposited in the GenBank/EMBL/DDBJ Bioproject database under the acces […]

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