README.md

In TheZetner/krakenreports: What the Package Does (One Line, Title Case)

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

TheZetner/krakenreports documentation built on March 30, 2021, 10:59 a.m.