Munch et al. (Syst Bio 2008) assign taxonomies to sequences with the BLAST+tree method, which produces not only a best-guess taxonomic assignment but also a posterior probability for each taxonomic level. The downsides to their implementation are (1) remote BLAST option only, which is slow, and (2) a complex HTML output, which impedes use of the taxonomic info for downstream analysis, such as the creation of OTU tables.
My feature request is to incorporate SAP (or a similar procedure) as an method option in assign_taxonomies.py and extracting the taxonomic info to put into OTU tables and into the query fasta file. SAP has a tendency to crash, so QIIME would need to add the ability to remove crash-causing sequences.
This new feature would expand the usefulness of QIIME for non-microbial datasets.
gregcaporaso
commented
11 years ago
Munch et al. (Syst Bio 2008) assign taxonomies to sequences with the BLAST+tree method, which produces not only a best-guess taxonomic assignment but also a posterior probability for each taxonomic level. The downsides to their implementation are (1) remote BLAST option only, which is slow, and (2) a complex HTML output, which impedes use of the taxonomic info for downstream analysis, such as the creation of OTU tables.
My feature request is to incorporate SAP (or a similar procedure) as an method option in assign_taxonomies.py and extracting the taxonomic info to put into OTU tables and into the query fasta file. SAP has a tendency to crash, so QIIME would need to add the ability to remove crash-causing sequences.
This new feature would expand the usefulness of QIIME for non-microbial datasets.