q2-minimap2

QIIME 2 Plugin for quality control and taxonomic classification of long sequences using Minimap2

Step 1: Create q2-minimap2 environment

mamba create -n q2-minimap2 -c conda-forge -c bioconda -c https://packages.qiime2.org/qiime2/2024.2/shotgun/passed/ -c defaults q2cli q2-types q2-feature-classifier minimap2 bs4 samtools

Step 2: Activate q2-minimap2 environment

conda activate q2-minimap2

Step 3: Installing python package

make dev
qiime dev refresh-cache

Step 4: Download input data

Datasets

Step 5: Execution

• build-index
  • Build Minimap2 index database

  qiime minimap2 build-index --i-sequences reference.qza --o-index-database index.qza --verbose

• minimap2-search

  • Generate both hits and no hits for each query. Keep a maximum of one hit per query (primary).

  qiime minimap2 minimap2-search --i-query-reads fasta_reads.qza --i-index-database database.qza --o-search-results paf.qza

  • Generate only hits for each query. Keep a maximum of one hit per query (primary mappings).

  qiime minimap2 minimap2-search --i-query-reads fasta_reads.qza --i-index-database database.qza --o-search-results paf_only_hits.qza

  • Generate only hits for each query. Keep a maximum of 10 hits per query.

  qiime minimap2 minimap2-search --i-query-reads fasta_reads.qza --i-index-database database.qza --p-maxaccepts 10 --p-output-no-hits False --o-search-results paf_only_hits_up_to_10_per_query.qza

• filter reads (fastq)

  • Keep mapped (single-end reads)

  qiime minimap2 filter-single-end-reads --i-query-reads reads.qza --i-index-database database.qza --o-filtered-query-reads mapped.qza --verbose

  • Keep unmapped (single-end reads)

  qiime minimap2 filter-single-end-reads --i-query-reads reads.qza --i-index-database database.qza --p-keep "unmapped" --o-filtered-query-reads unmapped.qza --verbose

  • Keep mapped reads with mapping percentage >= 85% (single-end reads)

  qiime minimap2 filter-single-end-reads --i-query-reads reads.qza --i-index-database database.qza --p-min-per-identity 0.85  --o-filtered-query-reads mapped_over_85p_id.qza --verbose

  • Using the reference sequences instead of the index database (single-end reads)

  qiime minimap2 filter-single-end-reads --i-query-reads reads.qza --i-reference-reads reference.qza --o-filtered-query-reads mapped.qza --verbose

• Extract sequences (fasta)
  • Extract mapped

  qqiime minimap2 extract-seqs --i-sequences fasta_reads.qza --i-index-database database.qza --p-extract "mapped" --o-extracted-seqs extracted_mapped.qza --verbose

  • Extract unmapped

  qiime minimap2 extract-seqs --i-sequences fasta_reads.qza --i-index-database database.qza --p-extract "unmapped" --o-extracted-seqs extracted_unmapped.qza --verbose

• classify-consensus-minimap2
  • Assign taxonomy to query sequences using Minimap2

  qiime minimap2 classify-consensus-minimap2 --i-index-database classification_input/index.qza --i-query classification_input/n1K_initial_reads_SILVA132.fna.qza --i-reference-taxonomy classification_input/raw_taxonomy.qza --p-num-threads 6 --output-dir outDir --verbose