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SOP 2. Sequence processing
| Processing step | Closed reference | Open reference | De novo |
|---|---|---|---|
| OTU picking | SortMeRNA vs GG97 v13.8 or Silva v123 | Sumaclust/SortMeRNA vs rep_set.fa | Swarm v2 |
| Taxonomy assignment | (comes with GG or Silva) | SortMeRNA | (same as open-ref) |
| Alignment | (comes with GG or Silva) | SSU-ALIGN(a) (not PyNAST) | (same as open-ref) |
| Tree building | (comes with GG or Silva) | FastTreeMP(b) | (same as open-ref) |
| Outputs (+Map) | BIOM, Taxonomy, Tree | BIOM, Taxonomy, Tree | BIOM, Taxonomy, Tree |
(a): Greg's preferred option. (b): With double precision.
echo "pick_subsampled_reference_otus_through_otu_table.py -i /home/shared/emp-isme14/study_1031_split_library_seqs_and_mapping/study_1031_split_library_seqs.fna,/home/shared/emp-isme14/study_1033_split_library_seqs_and_mapping/study_1033_split_library_seqs.fna,/home/shared/emp-isme14/study_1034_split_library_seqs_and_mapping/study_1034_split_library_seqs.fna,/home/shared/emp-isme14/study_1035_split_library_seqs_and_mapping/study_1035_split_library_seqs.fna,/home/shared/emp-isme14/study_1036_split_library_seqs_and_mapping/study_1036_split_library_seqs.fna,/home/shared/emp-isme14/study_1037_split_library_seqs_and_mapping/study_1037_split_library_seqs.fna,/home/shared/emp-isme14/study_1038_split_library_seqs_and_mapping/study_1038_split_library_seqs.fna,/home/shared/emp-isme14/study_1039_split_library_seqs_and_mapping/study_1039_split_library_seqs.fna,/home/shared/emp-isme14/study_1043_split_library_seqs_and_mapping/study_1043_split_library_seqs.fna,/home/shared/emp-isme14/study_1197_split_library_seqs_and_mapping/study_1197_split_library_seqs.fna,/home/shared/emp-isme14/study_1198_split_library_seqs_and_mapping/study_1198_split_library_seqs.fna,/home/shared/emp-isme14/study_1222_split_library_seqs_and_mapping/study_1222_split_library_seqs.fna,/home/shared/emp-isme14/study_1240_split_library_seqs_and_mapping/study_1240_split_library_seqs.fna,/home/shared/emp-isme14/study_1242_split_library_seqs_and_mapping/study_1242_split_library_seqs.fna,/home/shared/emp-isme14/study_1288_split_library_seqs_and_mapping/study_1288_split_library_seqs.fna,/home/shared/emp-isme14/study_1289_split_library_seqs_and_mapping/study_1289_split_library_seqs.fna,/home/shared/emp-isme14/study_1453_split_library_seqs_and_mapping/study_1453_split_library_seqs.fna,/home/shared/emp-isme14/study_1526_split_library_seqs_and_mapping/study_1526_split_library_seqs.fna,/home/shared/emp-isme14/study_632_split_library_seqs_and_mapping/study_632_split_library_seqs.fna,/home/shared/emp-isme14/study_638_split_library_seqs_and_mapping/study_638_split_library_seqs.fna,/home/shared/emp-isme14/study_659_split_library_seqs_and_mapping/study_659_split_library_seqs.fna,/home/shared/emp-isme14/study_662_split_library_seqs_and_mapping/study_662_split_library_seqs.fna,/home/shared/emp-isme14/study_678_split_library_seqs_and_mapping/study_678_split_library_seqs.fna,/home/shared/emp-isme14/study_723_split_library_seqs_and_mapping/study_723_split_library_seqs.fna,/home/shared/emp-isme14/study_776_split_library_seqs_and_mapping/study_776_split_library_seqs.fna,/home/shared/emp-isme14/study_808_split_library_seqs_and_mapping/study_808_split_library_seqs.fna,/home/shared/emp-isme14/study_809_split_library_seqs_and_mapping/study_809_split_library_seqs.fna,/home/shared/emp-isme14/study_810_split_library_seqs_and_mapping/study_810_split_library_seqs.fna,/home/shared/emp-isme14/study_925_split_library_seqs_and_mapping/study_925_split_library_seqs.fna,/home/shared/emp-isme14/study_933_split_library_seqs_and_mapping/study_933_split_library_seqs.fna -r /scratch/caporaso/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.fasta -o /home/shared/emp-isme14/ucrss_fast/ -aO 50 -n emp.isme14. -p /home/shared/emp-isme14/ucrss_params.txt" | qsub -k oe -N emp-otus -q norestrict -l nodes=1:ppn=60