HGA specifications


Unique identifier OMICS_11256
Name HGA
Alternative name Hierarchical Genome Assembly
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
SPAdes, Velvet
Maintained Yes


No version available



  • person_outline As Al-okaily

Publication for Hierarchical Genome Assembly

HGA citation


Draft Genome Sequence of the Plasmid Free Lactococcus lactis subsp. lactis Strain LMG 19460

Genome Announc
PMCID: 5399264
PMID: 28428305
DOI: 10.1128/genomeA.00210-17

[…] paired-end reads (totaling ~140× coverage). Paired-end reads were analyzed for Phred quality, trimmed and filtered using Fastq-Mcf version 1.04.676 (), and assembled using SPAdes version 3.8.0 () and HGA version 1.0 (). Generated contigs were scaffolded using SSPACE version 3.0 () followed by automated improvement using iCORN (). The L. lactis subsp. lactis LMG 19460 genome was assembled in 41 con […]

HGA institution(s)
Computer Science & Engineering Department, University of Connecticut, Storrs, CT, USA
HGA funding source(s)
This work has been partially supported by Agricud Food Research Initiative Competitive Grant no. 201167016-30331 from the USDA National Institute of Food and Agriculture.

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