/krakenreports

Create kmer visualizations from kraken output

Primary LanguageRMIT LicenseMIT

krakenreports

How to install:

Create a conda environment and then run the following

sbatch -p NMLResearch -c 1 --mem=4G --wrap="wget -O - https://raw.githubusercontent.com/TheZetner/krakenreports/master/inst/exec/install.sh | bash"
  • Sbatch is only necessary on slurm system
  • Runs install.sh which does the following
    • Installs...
      • kraken2 from bioconda
      • r-base from r
      • r-base from r
      • r-essentials from conda-forge
      • r-xml from conda-forge
    • Installs R Packages Remotes(CRAN) and Krakenreports(Github)
    • Copies executable scripts to the bin/ folder of your Conda environment

How to update (lazily)

To update krakenreports and its executable scripts run the following in your Conda environment.

sbatch -p NMLResearch -c 1 --mem=4G --wrap="wget -O - https://raw.githubusercontent.com/TheZetner/krakenreports/master/inst/exec/update.sh | bash"

Executable Scripts

runkraken.sh to run kraken2 via sbatch on a folder of fastq files
krakenreports.R to create plots and reports of the results

Results

Two Tables of Results

  • <PREFIX>_perseq.csv - Identified k-mer counts by taxonomy per read sequence
Status Sequence TaxonomicName Count
RUN1-kraken.tsv:C FAKE-READ-1 Unclassified 1741
RUN1-kraken.tsv:C FAKE-READ-1 Homo sapiens 268
RUN1-kraken.tsv:C FAKE-READ-1 Severe acute respiratory syndrome coronavirus 2 251
RUN1-kraken.tsv:C FAKE-READ-2 Unclassified 1219
RUN1-kraken.tsv:C FAKE-READ-2 Homo sapiens 246
RUN1-kraken.tsv:C FAKE-READ-2 Severe acute respiratory syndrome coronavirus 2 187
RUN1-kraken.tsv:C FAKE-READ-2 Coronaviridae 5
RUN1-kraken.tsv:C FAKE-READ-2 Severe acute respiratory syndrome-related coronavirus 5
RUN1-kraken.tsv:C FAKE-READ-3 Unclassified 1068
RUN1-kraken.tsv:C FAKE-READ-3 Homo sapiens 352
RUN1-kraken.tsv:C FAKE-READ-3 Severe acute respiratory syndrome coronavirus 2 305
RUN1-kraken.tsv:C FAKE-READ-3 Severe acute respiratory syndrome-related coronavirus 4
RUN2-kraken.tsv:C FAKE-READ-4 Unclassified 1108
RUN2-kraken.tsv:C FAKE-READ-4 Homo sapiens 338
RUN2-kraken.tsv:C FAKE-READ-4 Severe acute respiratory syndrome coronavirus 2 241
  • <PREFIX>_allseq.csv - Identified k-mer counts by taxonomy for all
TaxonomicName Count
Unclassified 11919
Homo sapiens 2850
Severe acute respiratory syndrome coronavirus 2 2000
Coronaviridae 63
Severe acute respiratory syndrome-related coronavirus 36
root 5
Beluga whale coronavirus SW1 2

Plot

Assorted Miscellaneous Ideas

Install alone via remotes:

Rscript --vanilla -e 'remotes::install_github("TheZetner/krakenreports")'

Sometimes it's worth linking files:

for i in `ls ../../<FOLDEROFFILES>/*-kraken.tsv`; do ln -s $i ./; done

Searching for human (9606) reads in kraken2 output:

grep -P "\s+9606\s+" -H *-kraken.tsv > human.tsv