Harvest specifications


Unique identifier OMICS_08468
Name Harvest
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format GGR,FASTA,VCF
Output data Compressed binary archive
Output format GGR,FASTA,VCF
Operating system Unix/Linux, Mac OS
Programming languages C++, Python, Shell (Bash)
Computer skills Advanced
Version 1.3
Stability Stable
Source code URL https://codeload.github.com/marbl/harvest/zip/v1.1.2
Maintained Yes


  • Gingr
  • HarvestTools
  • Parsnp



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  • person_outline Todd J. Treangen <>

Additional information


Publication for Harvest

Harvest in publications

PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] st131 isolates that represented the three reported st131 clades. a1_036_gull was identified as clade b and a1_001_gull was identified as clade a, based on a separate core genome analysis using parsnp (supplementary fig. ).table 1†nt = new sequence type., †nt = new sequence type., amr gene detection using srst2 identified a total of 27 different amr genes, three of which (amph, ampc2, mrda […]

PMCID: 5849743
PMID: 29535301
DOI: 10.1038/s41426-018-0033-1

[…] esbl genes, and all the esbl-ec isolates were analyzed to retrieve the esbl genotypes for further analysis. draft genome sequences were aligned and then applied for phylogenetic tree construction by parsnp in the harvest package, and the phylogenetic tree was visualized with figtree as previously described. sixty esbl-ec strains were randomly selected to conduct the pfge analysis using […]

PMCID: 5812336
PMID: 29479341
DOI: 10.3389/fmicb.2018.00150

[…] 2 enterobacter, glycogen synthesis cluster; (villa et al., )) were analyzed accordingly. the number of snps in the core genome between isolates of the same st was calculated using harvest suite 1.0 (parsnp) and mega 6.0 (http://www.megasoftware.net/)., this whole genome shotgun project has been deposited at ddbj/ena/genbank under the bioproject number prjna421654 (pjmh00000000 [imt38402], […]

PMCID: 5699109
PMID: 29162049
DOI: 10.1186/s12864-017-4299-9

[…] a maximum likelihood phylogenetic tree based on the core genome of e. faecium e745 and an additional 72 e. faecium strains representing the global diversity of the species [], was generated using parsnp [] with settings -c (forcing inclusion of all genome sequences) and -x (enabling recombination detection and filtering). the resulting phylogenetic tree was visualized using mega 7.0.26 []. […]

PMCID: 5715374
PMID: 29250039
DOI: 10.3389/fmicb.2017.02262

[…] were assembled using velvet 1.2.7. prokka v 1.10 was used for the annotation of plasmid genes; plasmidfinder (https://cge.cbs.dtu.dk/services/plasmidfinder/) was used to detect plasmid inc groups; parsnp (https://github.com/marbl/parsnp) was used to align the core genome. the resistance genes were identified by performing blastn against the resfinder 2.1 database […]

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Harvest institution(s)
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA
Harvest funding source(s)
Supported by an Agreement (No. HSHQDC-07-C-00020) awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC); and a Federally Funded Research and Development Center.

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