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Protocols

Hawkeye specifications

Information


Unique identifier OMICS_23190
Name Hawkeye
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Requirements
Qt
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Michael C. Schatz

Additional information


http://www.cbcb.umd.edu/~mschatz/Presentations/AMOS_Validation_Visualization.pdf

Publications for Hawkeye

Hawkeye citations

 (21)
library_books

Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

2017
PLoS One
PMCID: 5728499
PMID: 29236755
DOI: 10.1371/journal.pone.0188371

[…] apDos platform [] to detect C- and KS- domains, were used. Additionally, the identification of CRISPR repeats was carried out by the CRISPRFinder tool []. The assembly visualization was made with the Hawkeye tool from the AMOS open-source project Version 3.1.0 [] and Artemis []. The circular representation of the draft genome was built through the Circos software []. Finally, CDSs were considered […]

library_books

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote Eukaryote Interactions within the Pseudovibrio Genus

2016
Front Microbiol
PMCID: 4811931
PMID: 27065959
DOI: 10.3389/fmicb.2016.00387

[…] vich et al., ), employing varying kmers of 41, 55, 59, 71, 99, 127, and MismatchCorrector for improved output (Li and Durbin, ). Resulting contigs were inspected for misassembles with AMOS v3.1.0 and HAWKEYE v2.0 (Schatz et al., ). The genomes of strain AD2, WM33 (formally AD30), W64 (formally AD8), and W74 (formally AD15) were sequenced using an Illumina HiSeq sequencer. Reads were dynamically tr […]

library_books

Genome Sequence of Rapid Beer Spoiling Isolate Lactobacillus brevis BSO 464

2015
Genome Announc
PMCID: 4669400
PMID: 26634759
DOI: 10.1128/genomeA.01411-15

[…] iotechnology Institute (NRC PBI; Saskatoon, SK). Two separate runs yielded 330,771 unpaired and 567,735 paired reads for ~30× coverage. Reads were assembled using Newbler GS De Novo assembler v2.5.3. Hawkeye () was used to visualize the 236 contigs across 17 scaffolds to identify contigs that could be potentially joined by sequencing of PCR amplicons (via the NRC PBI ABI 3700xl platform).The Lb464 […]

library_books

De novo Genome Assembly of the Fungal Plant Pathogen Pyrenophora semeniperda

2014
PLoS One
PMCID: 3903604
PMID: 24475219
DOI: 10.1371/journal.pone.0087045

[…] assembly such as expansions or contractions of the reads that make up the assembly. Contig assemblies were imported into amosvalidate along with coordinates of the paired-end sequences for analysis. Hawkeye was used to visualize data from amosvalidate . The amosvalidate output data was imported into Hawkeye where each scaffold was visually inspected for assembly errors. […]

library_books

Phages of non dairy lactococci: isolation and characterization of ΦL47, a phage infecting the grass isolate Lactococcus lactis ssp. cremoris DPC6860

2014
Front Microbiol
PMCID: 3888941
PMID: 24454309
DOI: 10.3389/fmicb.2013.00417

[…] riophage DNA sequencing was performed using the Roche GS FLX+ system to >20× coverage (MWG, Ebersberg, Germany). The quality of the raw assembly reads were visualized and verified using the programme Hawkeye (Amos) (Schatz et al., ) and Consed (Gordon, ). To verify the genome structure, PCR amplicons were generated with the Platinum Hi-fidelity PCR Supermix (Invitrogen, Life Technologies, Dublin, […]

call_split

Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

2013
PMCID: 3960531
PMID: 24173459
DOI: 10.1038/ismej.2013.186
call_split See protocol

[…] were then merged using the minimus2 tool. This is an abridged version of the pipeline conceived and described by . Comparative evaluation of the output from these two different pipelines was done in Hawkeye (). MAUVE () was used to screen for evidence of genomic rearrangements. […]

Citations

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Hawkeye institution(s)
Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, University of Maryland, College Park, MD, USA; Department of Computer Science and Human-Computer Interaction Lab, A.V. Williams Building, University of Maryland, College Park, MD, USA
Hawkeye funding source(s)
Supported in part by NIH award R01-LM06845, the National Institute of Allergy and Infectious Disease under contract NIH-NIAIDDMID-04-34, HHSN266200400038C, and DHS/HSARPA award W81XWH-05-2-0051.

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