taxa assignment

Qiime Python assign_taxonomy.py

-m 分类注释算法，rdp, blast,rtax, mothur, uclust, sortmerna可选其中之一，默认uclust

Sample Assignment with BLAST

Taxonomy assignments are made by searching input sequences against a blast database of pre-assigned reference sequences. If a satisfactory match is found, the reference assignment is given to the input sequence. This method does not take the hierarchical structure of the taxonomy into account, but it is very fast and flexible. If a file of reference sequences is provided, a temporary blast database is built on-the-fly. The quality scores assigned by the BLAST taxonomy assigner are e-values.

To assign the sequences to the representative sequence set, using a reference set of sequences and a taxonomy to id assignment text file, where the results are output to default directory "blast_assigned_taxonomy", you can run the following command:""","""%prog -i repr_set_seqs.fasta -r ref_seq_set.fna -t id_to_taxonomy.txt"""))

Assignment with the RDP Classifier

To assign the representative sequence set, where the output directory is "rdp_assigned_taxonomy", you can run the following command:""","""%prog -i repr_set_seqs.fasta -m rdp"""))

Sample Assignment with RTAX

Taxonomy assignments are made by searching input sequences against a fasta database of pre-assigned reference sequences. All matches are collected which match the query within 0.5% identity of the best match. A taxonomy assignment is made to the lowest rank at which more than half of these hits agree. Note that both unclustered read fasta files are required as inputs in addition to the representative sequence file.

To make taxonomic classifications of the representative sequences, using a reference set of sequences and a taxonomy to id assignment text file, where the results are output to default directory "rtax_assigned_taxonomy", you can run the following command:""","""%prog -i rtax_repr_set_seqs.fasta -m rtax --read_1_seqs_fp read_1.seqs.fna --read_2_seqs_fp read_2.seqs.fna -r rtax_ref_seq_set.fna -t rtax_id_to_taxonomy.txt"""))

RTAX: Rapid and accurate taxonomic classification of short paired-end
      sequence reads from the 16S ribosomal RNA gene.

David A. W. Soergel (1), Rob Knight (2), and Steven E. Brenner (1)

1 Department of Plant and Microbial Biology,
  University of California, Berkeley 
2 Howard Hughes Medical Institute and Department of Chemistry 
  and Biochemistry, University of Colorado at Boulder
* Corresponding author (current address): soe...@cs.umass.edu

Version 0.984  (August 7, 2013)

http://dev.davidsoergel.com/rtax

Please cite:
Soergel D.A.W., Dey N., Knight R., and Brenner S.E.  2012.
Selection of primers for optimal taxonomic classification of
environmental 16S rRNA gene sequences.  ISME J (6), 1440–1444