- Integrated platforms: QIIME 2, SHOGUN
- Web servers: Qiita
- Sequence aligners: Bowtie2, BWA, Minimap2
- Sequence aligners: BLAST, VSEARCH
- Metagenomics profilers: Kraken/Bracken, Centrifuge, MetaPhlAn2, mOTUs2
- Genome databases: WoL, RefSeq, GTDB
- Taxonomic databases: NCBI, GTDB
- Functional databases: UniRef, GO, KEGG, BioCyc
Contents to be added. Some prelim documents are:
- https://github.com/biocore/wol/blob/master/start.md#information-for-users-of
- https://github.com/biocore/wol/blob/master/protocols/genome_database.md
The WoL database and the SHOGUN workflow are available at the Qiita server. Users can analyze shotgun metagenomic data using WoL from the graphic user interface:
- Start from host-filtered, adapter-trimmed per sample FASTQ files. Click "Process".
- In "Choose command:", select "Shogun v1.0.7".
- In "Parameter set:", select "wol_bowtie2" (or other combinations of aligner and database).
- Click "Add Command" to kick-start the SHOGUN workflow.
- When the job is completed, among the output files there is "Shogun Alignment Profile". It is a multiplexed, xzipped SAM format alignment file.
- Click "alignment.bowtie2.sam.xz" to download this file.
- You may now run Woltka by executing
woltka classify -i alignment.bowtie2.sam.xz ...
GTDB (Genome Taxonomy Database) (Parks et al., 2018) is a phylogeny-based taxonomy system for bacteria and archaea.
The GTDB taxonomy is provided as Greengenes-style lineage strings, therefore can be directly parsed by Woltka (the file gtdb_taxonomy.tsv can be found in the GTDB-Tk database):
woltka classify --lineage gtdb_taxonomy.tsv --rank phylum,genus,species ...More details and various options of using GTDB are provided here.