Kraken | Homology-Based Taxonomic

[…] 0.33 [] at the q20 level. reads containing ribosomal rna (rrna) sequences were erased from the dataset to avoid mis-annotation of rrnas as putative proteins [] using sortmerna version 2.0 []. the kraken taxonomic sequence classification system version 0.10.5 [] was applied to filter out prokaryotic sequences. those reads belong potentially to microorganisms co-inhabiting tree holes […]

[…] and trimmed at both 5’ and 3’ ends using trimmomatic [] to filter out reads of low quality (phred quality score <30, length <36 bp). potential contaminating sequences were checked using kraken []; sequencing errors were corrected using lighter []. corrected reads were de novo assembled with spades 3.5.0 []; assembly quality was evaluated by quast []. contigs of >200 bp […]

[…] protocol and sequenced on an illumina hiseq2000 device with 100-cycle paired-end runs to give an average depth of 85-fold. taxonomic identity was assigned to all short reads and assemblies using kraken []. multilocus sequence types (sts) were derived from illumina read data using an in-house tool, available at https://github.com/sanger-pathogens/mlst_check. de novo multi-contig draft […]

[…] 5 gb). trimmomatic v_0.36 was used to remove low quality sequences. human sequences were removed after alignment with reference genome (hg38 database []) using bowtie2 v_2.2.9, with default settings. kraken v_0.10.5-beta was then used to for taxonomic classification of unmapped microbial reads []. by the default setting of kraken, only complete genome sequences were included as the reference genom […]

[…] within the galaxy platform, with a galaxy web server instance supported by the national microbiology laboratory, public health agency of canada (phac nml galaxy). a custom workflow integrating kraken taxonomic classification tools and the amrplusplus resistome analysis pipeline tools was setup in galaxy to obtain simultaneous outputs for both resistome and microbiome analyses […]

[…] 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, […]

[…] 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 […]

[…] 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) ()., samples were stored at −80°c prior to analysis. urine samples were subjected to vortex mixing and then centrifuged at 1,600 × g for 10 min […]

[…] databases maintained within a research group, into an analysis pipeline. additional plugins were implemented to support the most recent tools used for metagenome analysis, such as centrifuge, kraken, or ghostx. finally, the well-known mothur and qiime suites have recently been integrated into conveyor, extending the applicability of mgx from metagenomes to the analysis of 16s rrna […]

[…] have been developed to reduce this time by using alternatives to classical alignment. one approach is to match k-mers with a reference, as used in facs (stranneheim et al., ), lmat (ames et al., ), kraken (wood and salzberg, ), taxonomer (flygare et al., ), and metlab (norling et al., ). exact k-mer matching is generally faster than alignment, but requires a lot of computer memory. another […]