Quake protocols

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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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  • person_outline David Kelley <>

Publication for Quake

Quake in pipelines

 (20)
2017
PMCID: 5420552
PMID: 28533767
DOI: 10.3389/fmicb.2017.00789

[…] 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 […]

2017
PMCID: 5550751
PMID: 28790205
DOI: 10.1128/mBio.00822-17

[…] with lengths of 100, 125, and 150 bp. for each sample, reads were assessed with the fastqc tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were filtered by quake (). all of the assemblies were performed by abyss with different k-mers (); the best assembly for each strain, with the largest scaffold n50, was annotated by prokka ()., all b. thuringiensis […]

2017
PMCID: 5624745
PMID: 28963199
DOI: 10.1128/genomeA.00691-17

[…] 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 […]

2016
PMCID: 4832150
PMID: 27081122
DOI: 10.1128/genomeA.00185-16

[…] inc., san diego, ca), and paired-end sequencing was performed with the illumina miseq platform, using 600-cycle miseq reagent kits (version 3). sequencing errors in reads were corrected using quake version 0.3, with a k-mer size of 15 (), and assembled de novo using spades version 3.5 (). contigs <1,000 bp were excluded from the analysis. gene predictions and annotations were performed […]

2016
PMCID: 4848470
PMID: 27120974
DOI: 10.1038/srep24863

[…] from the truseq adapters, an in-house script to remove low quality portions (quality score <20) at the ends of both reads, jellyfish to obtain k-mer frequencies in all the libraries, and quake to correct sequencing errors. the data processing resulted in seven libraries that were supplied to platanus for genome assembly: 250 bp and 500 bp paired-end libraries, 2 kbp, 6kbp, 15k bp […]


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Quake in publications

 (69)
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] were downloaded and used for gene prediction in ap, plat_d, merge, and plat*_gc assemblies., 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 […]

PMCID: 5753508
PMID: 29298673
DOI: 10.1186/s12864-017-4407-x

[…] 0 bp insert size) and a mate-pair (5 kb insert size) library were used. in total 7.48 and 7.50 gbp high quality data were generated for vl1 and vl2, respectively. all reads were error corrected using quake v0.3.4 []., first, the illumina reads from vl1 and vl2 were mapped to the v. dahliae reference genome (gca_000400815.2), based on strain jr2 [] using bwa-mem v0.7.8 [] with default settings. var […]

PMCID: 5656584
PMID: 29070832
DOI: 10.1038/s41598-017-14335-7

[…] ends with quality scores lower than q20 were trimmed. the potential nucleotide differences were validated using breseq version 0.28. for structural variations, the sequence reads were analyzed using quake, and de novo assembly was performed using soapdenovo. the contigs were mapped on the genome using blast to screen candidates for indels. the de novo assembly near the candidate sites […]

PMCID: 5624745
PMID: 28963199
DOI: 10.1128/genomeA.00691-17

[…] 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 […]

PMCID: 5624746
PMID: 28963200
DOI: 10.1128/genomeA.00740-17

[…] study., genomic dna of ygd22-03 was extracted and a 500-bp paired-end insert library was sequenced on an illumina hiseq 2500 platform with read lengths of 150 bp. the reads were quality filtered by quake (), resulting in a 2.169-gbp total length that comprised 17,358,564 high-quality reads and represented 400-fold coverage of the genome. the clean reads were then de novo assembled with a spades […]


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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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