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Information
| Unique identifier | OMICS_04481 |
|---|---|
| Name | Kraken |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux |
| Programming languages | C++, Perl |
| Computer skills | Advanced |
| Stability | Stable |
| Maintained | Yes |
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Publication for Kraken
Kraken citations
(167)American Gut: an Open Platform for Citizen Science Microbiome Research
[…] e were dropped. The characterization of the metabolites from the supernatant using HPLC-MS is discussed under “HPLC-MS analysis” above.Following assembly of the draft genomes, taxonomic assessment by Kraken () revealed that of the 119 successfully sequenced colony isolate cultures, 95 matched the bloom organisms identified by Amir et al. (). Compellingly, 70 of these isolate genomes contained exac […]
Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant
[…] 300 bp were then excluded from the final assembly. The statistical results of the assembly were estimated using QUAST (version 3.2) [].To examine sequencing reads for potential contamination, we used Kraken (version 1.0) [] with the standard Kraken database to check the paired-end DNA libraries. Classified reads reported by Kraken were further examined using our proposed pipeline (). Briefly, we e […]
Isolation of Oropouche Virus from Febrile Patient, Ecuador
[…] –40 borderline, >40 negative) and negative results for the other pathogens. As an initial screen for other pathogens, we applied unbiased metagenomic sequencing. Analysis of sequencing reads by using Kraken, a system for assigning taxonomic labels to individual reads (), identified 1% reads (5,016 of 464,444) as specific to OROV. We generated an OROV consensus sequence by mapping reads to a refere […]
Draft Genome Sequence of Plant Growth Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize
[…] uenced at MicrobesNG (http://www.microbesng.uk) using Illumina MiSeq and HiSeq 2500 technology platforms, with 2 to 250-bp paired-end reads. The closest existing reference genome was determined using Kraken (), and the reads were mapped using the Burrows-Wheeler Aligner (BWA) MEM algorithm (http://bio-bwa.sourceforge.net) to assess data quality. The reads were assembled by de novo assembly using S […]
A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults
[…] ic pathways produced by HUMAnN2 were derived from the MetaCyc database () and were the basis for analyses performed on microbial metabolic profiling. Taxonomic profiling was facilitated by use of the Kraken taxonomy assignment software tool (V.0.10.6) (). […]
Flexible metagenome analysis using the MGX framework
[…] axonomic classification workflow and compared its results to those of several established standalone tools, which were selected based on recency and reported frequency of use according to literature: Kraken [], Kaiju [], Centrifuge [], and MetaPhlAn 2 []. All tools were run with their respective default settings, with databases generated in May 2017, and classification performance was assessed at […]
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