Annotating reads

This workflow can be used to map reads to ICTV geomes. This might come in handy in instances where the virus abundance is extreamly low (clinical samples).

skadi reads -in <reads1>.fastq [-in2 <reads2.fastq>] -o outdir

Additional bbmap and pileup options can be used to customize this workflow.

Usage: skadi reads [OPTIONS] [SNAKEMAKE_ARGS]...

  SKADI: Sequence-based Knowledgebase for Annotation, Detection, and Identification
  application designed to  provide taxonomy annotations to virus contigs and
  mapping reads directly to virus genomes.

  usage (paired-end): skadi reads [OPTIONS] -i1 pair1.fastq -i2 pair2.fastq -o
  mapping_results.tsv

  usage (single-end): skadi reads [OPTIONS] -i1 pair1.fastq -o
  mapping_results.tsv

Options:
  -in, --input PATH    input read file1 to run skadi on  [required]
  -in2, --input2 PATH  input read file2 (paired-end) to run skadi on
  -o, --output PATH    dir to store skadi results  [required]
  -j, --jobs INTEGER   use at most this many jobs in parallel (see cluster
                       submission for more details).  [default: 28]
  --bbmap_args TEXT    Extra arguments passed directly to BBMap (e.g.
                       'minid=0.95 maxindel=3')  [default: nodisk=t minid=0.95
                       maxindel=2 -Xmx20g]
  --pileup-args TEXT   Extra arguments passed to pileup.sh / CoveragePileup
                       (e.g. 'minmapq=20 minbaseq=20 mincov=2 secondary=f
                       delcov=f')  [default:  qtrim=t trimq=10 border=5
                       secondary=f delcoverage=f minmapq=20]
  --summary-args TEXT  coverage percentage = cpAverage fold = afMin total
                       reads = mtr-cp 50.0 af 1 mtr 100  [default:  -cp 0.5
                       -af 1 -mtr 100]
  --profile TEXT       snakemake profile e.g. for cluster execution.
  -n, --dryrun         Test execution.
  -h, --help           Show this message and exit.

Results

Results can be found in the results directory within the output directory. A typical layout is:

├── input.coverage.tsv
├── input.pileup.tsv
├── input.sorted.bam
└── input.sorted.bam.bai

  • input.skadi.tsv contains summary of all reads mapped to reference virus genomes.

  • input.pileup.tsv contains pileup output.

  • input.sorted.bam sorted bam file.

  • input.sorted.bam.bai index of the sorted bam file.