Read classification analysis mode

• Perform a direct blast homology search using megablast (--megablast).

  Example 1 using a viral database:

  # Check for presence of adapters.
  # Perform a direct read homology search using megablast against a viral database.
  
  nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                              --adapter_trimming \
                              --analysis_mode read_classification \
                              --megablast \
                              --blast_threads 8 \
                              --blast_mode localdb \
                              --blastn_db /path/to/local_blast_db
  

  Example 2 using NCBI nt:

  # Check for presence of adapters .
  # Perform a direct read homology search using megablast and the NCBI NT database. 
  # You will need to download a local copy of the NCBI NT database. 
  # The blast search will be split into several jobs, containing 10,000 reads each, that will run in parallel. 
  # The pipeline will use 8 cpus when running the blast process.
  
  nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                              --adapter_trimming \
                              --analysis_mode read_classification \
                              --megablast \
                              --blast_threads 8 \
                              --blast_mode ncbi \ #default
                              --blastn_db /path/to/ncbi_blast_db/nt
  

• Perform a direct taxonomic classification of reads using Kraken2 and/or Kaiju.
  Example:

  # Check for presence of adapters
  # Perform a direct taxonomic read classification using Kraken2 and Kaiju. 
  # You will need to download Kraken2 index (e.g. PlusPFP) and Kaiju indexes (e.g. kaiju_db_rvdb).
  
  nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                              --adapter_trimming \
                              --analysis_mode read_classification \
                              --kraken2 \
                              --krkdb /path/to/kraken2_db \
                              --kaiju \
                              --kaiju_dbname /path/to/kaiju/kaiju.fmi \
                              --kaiju_nodes /path/to/kaiju/nodes.dmp \
                              --kaiju_names /path/to/kaiju/names.dmp
  

• Perform direct read homology search using megablast and the NCBI NT database and direct taxonomic read classification using Kraken2 and Kaiju.
  Example:

  # Check for presence of adapters
  # Filter reads against reference host
  # Perform a direct read homology search using megablast and the NCBI NT database.
  # Perform a direct taxonomic read classification using Kraken2 and Kaiju.
  nextflow run eresearchqut/ontvisc -resume -profile {singularity, docker} \
                              --adapter_trimming \
                              --host_filtering \
                              --host_fasta /path/to/host/fasta/file \
                              --analysis_mode read_classification \
                              --kraken2 \
                              --krkdb /path/to/kraken2_db \
                              --kaiju \
                              --kaiju_dbname /path/to/kaiju/kaiju.fmi \
                              --kaiju_nodes /path/to/kaiju/nodes.dmp \
                              --kaiju_names /path/to/kaiju/names.dmp \
                              --megablast --blast_mode ncbi \
                              --blast_threads 8 \
                              --blastn_db /path/to/ncbi_blast_db/nt