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Quake specifications

Information


Unique identifier OMICS_01106
Name Quake
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Kelley

Publication for Quake

Quake citations

 (59)
library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] Before genome assembly, duplicate Illumina reads were removed by FastUniq []. Reads were corrected using Quake [] with the following parameters: minimum length of reads ≥ 70 bp and minimum quality ≥ 20. The filtered reads were used to identify heterozygosity using JELLYFISH [] with –m 19 option and with […]

call_split

Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04 02, a Strain Toxic to Plutella xylostella

2017
Genome Announc
PMCID: 5624745
PMID: 28963199
DOI: 10.1128/genomeA.00691-17
call_split See protocol

[…] iSeq2500 with a paired-end library (insert size, 500 bp) strategy with read lengths of 150 bp. A total of 20,590,086 reads were obtained by Illumina sequencing, and low-quality reads were filtered by Quake (). The clean reads were de novo assembled by SPAdes 3.5.0 () into 51 contigs. The assembly was further improved by comparing it with the complete genome sequences of the other strains in this s […]

library_books

Evolution of the Largest Mammalian Genome

2017
Genome Biol Evol
PMCID: 5569995
PMID: 28854639
DOI: 10.1093/gbe/evx113

[…] WGS data were trimmed with trimmomatic version 0.36, respectively, using the same settings as for the RNAseq data detailed above. We then used the k-mer based approach of quake () to identify and filter reads in the WGS data. K-mers are sequence motifs of size k, and their analysis can provide insights into genome size and redundancy, and also sequencing error. In high […]

library_books

Resurgence of cucurbit downy mildew in the USA: Insights from comparative genomic analysis of Pseudoperonospora cubensis

2017
Ecol Evol
PMCID: 5574870
PMID: 28861228
DOI: 10.1002/ece3.3194

[…] Aylor, Price, & Carbone, ; Monacell & Carbone, ; Price & Carbone, ) previously for read filtering and variant discovery (Figure ) was used in this study. Raw sequence reads were error‐corrected using Quake (Kelley, Schatz, & Salzberg, ) and filtered based on a Phred‐quality score >20 using the FASTX‐Toolkit (Gordon & Hannon, ). Filtered read pairs were interleaved into a single FASTQ file using th […]

call_split

Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development

2017
Genetics
PMCID: 5560785
PMID: 28630114
DOI: 10.1534/genetics.117.203521
call_split See protocol

[…] d command line main options) are summarized in Table S4. Raw reads were trimmed for adaptors using Cutadapt () and low-quality bases, then corrected for sequencing errors based on k-mer content using Quake () and JELLYFISH (). Raw data were checked with FastQC () and a preliminary assembly generated with CLC Assembly Cell (CLC bio 2017) (Table S5). The CLC assembly was screened for contaminants us […]

library_books

Characterization of Mycobacterium chelonae Like Strains by Comparative Genomics

2017
Front Microbiol
PMCID: 5420552
PMID: 28533767
DOI: 10.3389/fmicb.2017.00789

[…] 5), and M. chelonae ATCC 35752T (accession number CP010946) were retrieved from the GenBank database (http://www.ncbi.nlm.nih.gov/genbank/). Sequencing errors in reads were corrected with the program Quake v0.3 (Kelley et al., ) and reads trimmed with the program Trimmomatic v0.33 (Bolger et al., ). The assembly was performed with Newbler program v3.0 (20140318_1550)—version with support for reads […]

Citations

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Quake institution(s)
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Quake funding source(s)
Supported by NIH grants R01-LM006845 and R01-GM083873.

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