Assemblathon protocols

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Assemblathon specifications

Information


Unique identifier OMICS_14889
Name Assemblathon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
qstaq.pl, FAlite.pm
Maintained Yes

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Maintainer


  • person_outline Keith Bradnam <>

Publications for Assemblathon

Assemblathon in pipelines

 (2)
2017
PMCID: 5436433
PMID: 28521789
DOI: 10.1186/s13059-017-1213-3

[…] of s. aureus and r. sphaeroides. other assembly reconciliation tools used the assemblathon dataset [], which was a similar assembly competition to gage. for instance, metassembler used both the assemblathon 1 and assemblathon 2 datasets., all assembly reconciliation tools were run with default parameters, and quast [] was used to gather extensive assembly statistics (see for details). […]

2016
PMCID: 4828583
PMID: 27148174
DOI: 10.3389/fmicb.2016.00469

[…] orfs in the selected assembled draft genomes., assembly of reads was performed using genovo with 50 iterations (laserson et al., ). the general assembly statistics of contigs were calculated using assemblathon_stats.pl. the percentage of assembly was calculated by aligning contigs to the genomic sequences of the selected genomes with default parameters using “bwa-mem” (version 0.5.9) […]


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Assemblathon in publications

 (61)
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…]  v.44837 (http://software.broadinstitute.org/allpaths-lg/blog/) [, ] using the trimmed/normalized short-pair reads and the nextclip processed mate-pair reads. assembly statistics were collected using assemblathon_stats.pl []. gaps in the scaffolds were then filled in by mapping the reads to the allpaths-lg scaffolds and seqman ngen software (dnastar inc., madison, wisconsin, usa)., alternatively, […]

PMCID: 5907361
PMID: 29669603
DOI: 10.1186/s12915-018-0508-5

[…] escherichia coli-, yeast-, and phage-contaminated reads. the reads of a. astaci and a. stellatus were assembled using masurca, version 2.0 [], and the assembly metrics were calculated using the assemblathon_stats.pl script []., the assembled data of aphanomyces were annotated with augustus v2.757 [] trained with the assembled rna-seq transcript generated in this study and the publicly […]

PMCID: 5901865
PMID: 29661185
DOI: 10.1186/s12915-018-0509-4

[…] [] (additional file : supplementary methods; additional file : figure s17)., the n50 scaffold lengths of the genome assemblies of p. picta and other reptiles were computed using the perl script assemblathon_stats.pl [] developed by the assemblathon project []. cegma v2.5 [] referring to the cvg [] was utilized in order to assess the completeness of the assemblies. for the cegma runs, […]

PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] after scaffolding, shotgun sequences were used to close gaps between contigs., to obtain genome assembly statistics, for each draft assembly we removed contigs shorter than 500 bp and used the assemblathon 2 script. contig break was set to 25 bp. for historical reasons, we also used cegma v.2.5 to determine the proportion of a defined core set of 248 highly conserved eukaryotic genes […]

PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] 12gb ram. each merge iteration took approximate 5 days and after five iterations, the assembly converged., the statistics for the four assemblies (ap, plat_d, merge and plat*_gc) were obtained using assemblathon script [] and the 486,205,130 base pair (bp) size of the v. vinifera reference genome (pn40024 12x.v2) was used for genome size estimation value []. total assemblathon statistics […]


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Assemblathon institution(s)
Genome Center, UC, Davis, CA, USA; Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; [etc]
Assemblathon funding source(s)
This work was supported by Wellcome Trust grant WT098051; ENCODE DAC (data analysis center) subaward on NHGRI grant no. U01HG004695 to the European Bioinformatics Institute; ENCODE DCC (data coordination center) NHGRI grant no. U41HG004568; Browser (Center for Genomic Science) NHGRI grant no. P41HG002371; GENCODE subaward on NHGRI grant no. U54HG004555 to the Sanger Center; NCI 1U24CA143858-01; NIH HG00064; PTDC/BIA-BEC/100616/2008; PTDC/EIA-EIA/100897/ 2008; the Fundacao para a Ciencia e Tecnologia; National Natural Science Foundation of China (30725008; 30890032; 30811130531; 30221004); a National Basic Research Program of China (973 program no. 2011CB809200); the Chinese 863 program (2006AA02Z177; 2006AA02Z334; 2006AA02A302; 2009AA022707); NSF, Major Research Instrumentation grant DBI 0821263 (University of Georgia, the Georgia Advanced Computing Resource Center), and NSF EF-0949453.

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