Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

BMC Bioinformatics

Table 11 Summary of ribodbmaker pass/fail outcomes for Yarza(SSU), SilvaMicrosporidia(SSU), SilvaRef(LSU), and SilvaParc(LSU) datasets

Dataset/test	Yarza pass/fail	SilvaMicrosporidia pass/fail	SilvaRef pass/fail	SilvaParc pass/fail
Ambiguous nucleotides	8493/277	1435/26	2928/65	385607/8640
Specified species	7543/1227	774/687	2089/904	204923/189324
Vector contamination	8735/35	460/1	2989/4	393938/305
Self-repeats	8635/135	1418/43	2929/64	390305/3942
Ribotyper	8085/685	1140/321	2925/68	145450/248797
Riboaligner	7720/1050	998/463	1583/1410	135252/258995
Length in range?	7617/103	957/41	1187/396	132984/2268
Expected span?	7612/5	669/288	990/197	103016/29968
All 1-sequence tests?	6359/2411	405/1056	759/2234	70127/324120
Ingroup analysis (many)	5158/1201	288/117	649/110	56606/13521
Ingroup analysis (1)	3246/3113	136/269	478/281	7129/52998

All tests except the ingroup analysis depend only on the sequence being tested. The four tests for ambiguous nucleotides, specified species, vector contamination, and self-repeats are done on all sequences, so sequences may fail more than one test. Only sequences that pass the ribotyper test are eligible as input to riboaligner. Only sequences that pass the riboaligner test are eligible to be tested for length and alignment span. Only sequences that pass all 1-sequence tests are eligle for ingroup analysis. The ingroup analysis can be done allowing many sequences from the same taxon to pass or limiting to 1 the number of sequences that pass from each taxon (argument --fione). The many option is a more meaningful test; we show the 1 option just for comparison. Data and instructions for reproducing these comparisons are available at https://github.com/nawrockie/ribovore-paper-2021-supplementary-material

ISSN: 1471-2105