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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




No version available

Publication for Hierarchical Genome-Assembly Process

HGAP citations


Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

Genome Announc
PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18
call_split See protocol

[…] o RSII platform was 23,264 (71.33-fold coverage), whereas the Illumina MiSeq platform provided 653,569 (121.27-fold coverage) short reads.De novo genome assembly of long reads was performed using the Hierarchical Genome Assembly Process version 3 (HGAP3) implemented in the SMRT analysis algorithm version 2.3.0 (). Different stages of the process involved preassembly, de novo assembly with Celera A […]


Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D 401

Genome Announc
PMCID: 5920184
PMID: 29700149
DOI: 10.1128/genomeA.00311-18

[…] y using 2 single-molecule real-time (SMRT) cells with 240-minute collection times. Sequencing reads were processed, mapped, and assembled with the Pacific Biosciences SMRT analysis pipeline using the HGAP3 protocol and polished using Quiver (). A total of 1.5 Gb of sequencing data was assembled into a single closed circular genome of 4,266,286 bp with 290.26-fold coverage. The assembled sequence w […]


Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South South Korea

Genome Announc
PMCID: 5920192
PMID: 29700134
DOI: 10.1128/genomeA.00194-18

[…] uencing platform at ChunLab (Seoul, South Korea). The bacterial genome was assembled de novo into four contigs, with an average genome coverage of 230.9×, using the PacBio SMRT Portal (2.3.0) and the Hierarchical Genome Assembly Process (HGAP) (). The Prokaryotic Genome Annotation System (Prokka) pipeline was used for genome annotation (). The data were submitted to the Rapid Annotations using Sub […]


Complete Genome Sequence of a Putative New Bacterial Strain, I507, Isolated from the Indian Ocean

Genome Announc
PMCID: 5908934
PMID: 29674539
DOI: 10.1128/genomeA.00246-18
call_split See protocol

[…] using PacBio long-read sequencing technology. A PacBio standard genomic library was sequenced on single-molecule real-time (SMRT) Cell 1M version 2.0. De novo genome assembly was performed using the Hierarchical Genome Assembly Process (HGAP) version 3.0 (). The assembled genome was submitted to the NCBI Prokaryotic Genome Annotation Pipeline for gene annotation ().Finally, there were 72,791 subr […]


Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

Genome Announc
PMCID: 5908946
PMID: 29674543
DOI: 10.1128/genomeA.00265-18

[…] 1.0 according to the manufacturer’s instructions, and sequencing was performed using 10 single-molecule real-time (SMRT) cells on the PacBio RS II platform. Genomic sequences were assembled using the Hierarchical Genome Assembly Process version 3 (HGAP3) pipeline embedded in PacBio SMRT Portal version (). Filtered subreads were aligned to contigs using BLASR (), and the corrected c […]


Draft Whole Genome Sequence of the Fluorene Degrading Sphingobium sp. Strain LB126, Isolated from a Polycyclic Aromatic Hydrocarbon Contaminated Soil

Genome Announc
PMCID: 5897811
PMID: 29650572
DOI: 10.1128/genomeA.00249-18

[…] ry was prepared and sequenced on one single-molecule real-time (SMRT) cell at the Génome Québec Innovation Centre (McGill University, Montréal, Canada). The de novo assembly was carried out using the Hierarchical Genome Assembly Process (HGAP)/Quiver protocol in SMRT Portal version (). The sequencing generated 734,729,152 bp from 98,542 subreads, with an average subread length of 8 […]


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

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