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Protocols

KmerGenie specifications

Information


Unique identifier OMICS_30268
Name KmerGenie
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.7048
Stability Stable
Source code URL http://kmergenie.bx.psu.edu/kmergenie-1.7048.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Paul Medvedev

Publication for KmerGenie

KmerGenie citations

 (63)
call_split

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

2018
Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w
call_split See protocol

[…] ree consecutive iterations following a Meta-assembly approach (Table ). First, both libraries were assembled together in parallel, using a k-mer size of 63 (when available) following the results from KmerGenie, by five assemblers: ABySS, Velvet, SOAPdenovo2, ALLPATHS-LG, MaSuRCA. The MaSuRCA assembler was run twice, once running the adapter filtering function (here termed “MaSuRCA-filtered”), the […]

library_books

A guide to sequence your favorite plant genomes

2018
Appl Plant Sci
PMCID: 5895188
PMID: 29732260
DOI: 10.1002/aps3.1030

[…] on than the mean coverage, and show up as a high frequency shoulder toward the right of the frequency plot (Fig. B). K‐mer plots can be generated by the Jellyfish package (Marçais and Kingsford, ) or KmerGenie (Chikhi and Medvedev, ), from where a few lines of R script can then be used to estimate the genome size (for tutorials see http://bioinformatics.uconn.edu/genome-size-estimation-tutorial/). […]

library_books

Full length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub genomic RNAs

2018
PLoS One
PMCID: 5832266
PMID: 29494671
DOI: 10.1371/journal.pone.0193682

[…] ps://github.com/iontorrent/TMAP) to evaluate coverage depth for each sample, Mira assembly [] was ran on uncleaned, downsampled reads to a mean coverage depth of 80 after best kmer size estimation by kmergenie []. Spades assemblies [] were performed after Trimmomatic cleaning.Contigs were aligned and reordered to the reference sequence with Mauve []. Unrelated contigs were removed. Viral contigs n […]

library_books

The End of a 60 year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton

2018
PMCID: 5873915
PMID: 29487186
DOI: 10.1534/g3.117.300429

[…] converted to a bam and coordinate sorted using SAMtools (). Reads not mapping to the D. magna reference were extracted using SAMtools.To identify the optimal k-mer value for de novo assembly, we used KmerGenie (). We utilized two different de novo assemblers for the trimmed, unmapped paired-end reads: Velvet v.1.2.10 () and SPAdes v.3.9.0 (). Contigs were scaffolded using the BESST scaffolding app […]

library_books

Characterization of plasmids harboring blaCTX M and blaCMY genes in E. coli from French broilers

2018
PLoS One
PMCID: 5779644
PMID: 29360838
DOI: 10.1371/journal.pone.0188768

[…] hich is used in Illumina sequencing in case of very redundant samples. The phiX174 unaligned reads were downsampled to fit a global coverage estimation of 80 times. After best kmer size estimation by KmerGenie [], SPAdes 3.1.1 (20) and MIRA 4.0rc1[] assemblers were run on Trimmomatic [] cleaned reads and raw reads, respectively. Redundant or poorly covered contigs were filtered out of assemblies. […]

library_books

Genomic repeats, misassembly and reannotation: a case study with long read resequencing of Porphyromonas gingivalis reference strains

2018
BMC Genomics
PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] []; MIRA (v4.0.2) []; PERGA (v0.5.03.02) []; SOAPdenovo (v2.04) []; SPAdes (v3.10.1) []; and Velvet (v1.2.10) []. For CCA and Geneious, reads were preassembled with PEAR (v0.9.10) []. Where required, KmerGenie (v1.7016) was used to determine the k-mer length parameter [].After the initial test step, we selected three software packages for assembly of all 24 genomes. The first was A5-miseq, in whic […]

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KmerGenie institution(s)
Department of Computer Science and Engineering, University Park, PA, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA

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