HGAP pipeline

HGAP specifications


Unique identifier OMICS_05136
Alternative names Hierarchical Genome-Assembly Process, HGAP3, HGAP2, SMRT Analysis HGAP3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for Hierarchical Genome-Assembly Process

HGAP citations

PMCID: 5809850

[…] and qubit 2.0 fluorometer (life technologies, usa). the genome of l. acidophilus la1 was sequenced with the pacbio rs ii (menlo park, usa) sequencing platform., genome assembly was performed using hgap 3.0 (chin et al., 2013), with default options. the start position of the chromosome was determined by the location of the gene encoding the chromosomal replication initiation protein, dnaa, […]

PMCID: 5620268

[…] of 87,287 polymerase reads, with a mean read length of 11,530 bp, were generated, resulting in a total of 1,006,456,227 bases with a 104-fold average coverage. the dna contigs were assembled using hgap 2.0 [37]. open reading frames and pseudogenes were predicted using rast 2.0 [38], combined with blastp/blastn [39] searches against the uniprotkb/swiss-prot [40] and refseq [41] databases. […]

PMCID: 5522923

[…] symptoms, including cough, pleuropneumonia, and lung lesion, in china in 2013., the whole genome was sequenced using the pacbio platform and resulted in a total of 657.9 mb after filtering raw data. hgap (2) was used for de novo assembly and resulted in a circular chromosome of 1,016,663 bp with a 23.67% g+c content, representing a sequencing coverage of 647×. the complete genome was analyzed […]

PMCID: 4175631

[…] (~1,100×, or 22× the median coverage) of all assemblies while the assemblies that relied on only miseq data have the highest maximum coverage (~15,000×, or 300× the median coverage) (figure 5). the hgap2 assembly is also the only assembly to have noticeable peaks in the coverage distribution reflecting collapsed repeats including the mitochondria and rrna as discussed above. it is less clear […]

HGAP institution(s)
Pacific Biosciences, Menlo Park, CA, USA

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