1 //uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
7 "uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime]\n"
8 " [--uchimealns results.alns]\n"
14 " Query sequences in FASTA format.\n"
15 " If the --db option is not specificed, uchime uses de novo\n"
16 " detection. In de novo mode, relative abundance must be given\n"
17 " by a string /ab=xxx/ somewhere in the label, where xxx is a\n"
18 " floating-point number, e.g. >F00QGH67HG/ab=1.2/.\n"
21 " Reference database in FASTA format.\n"
22 " Optional, if not specified uchime uses de novo mode.\n"
24 " ***WARNING*** The database is searched ONLY on the plus strand.\n"
25 " You MUST include reverse-complemented sequences in the database\n"
26 " if you want both strands to be searched.\n"
29 " Minimum abundance skew. Default 1.9. De novo mode only.\n"
30 " Abundance skew is:\n"
31 " min [ abund(parent1), abund(parent2) ] / abund(query).\n"
33 "--uchimeout filename\n"
34 " Output in tabbed format with one record per query sequence.\n"
35 " First field is score (h), second field is query label.\n"
36 " For details, see manual.\n"
38 "--uchimealns filename\n"
39 " Multiple alignments of query sequences to parents in human-\n"
40 " readable format. Alignments show columns with differences\n"
41 " that support or contradict a chimeric model.\n"
44 " Mininum score to report chimera. Default 0.3. Values from 0.1\n"
45 " to 5 might be reasonable. Lower values increase sensitivity\n"
46 " but may report more false positives. If you decrease --xn,\n"
47 " you may need to increase --minh, and vice versa.\n"
50 " Minimum divergence ratio, default 0.5. Div ratio is 100%% - \n"
51 " %%identity between query sequence and the closest candidate for\n"
52 " being a parent. If you don't care about very close chimeras,\n"
53 " then you could increase --mindiv to, say, 1.0 or 2.0, and\n"
54 " also decrease --min h, say to 0.1, to increase sensitivity.\n"
55 " How well this works will depend on your data. Best is to\n"
56 " tune parameters on a good benchmark.\n"
59 " Weight of a no vote, also called the beta parameter. Default 8.0.\n"
60 " Decreasing this weight to around 3 or 4 may give better\n"
61 " performance on denoised data.\n"
64 " Pseudo-count prior on number of no votes. Default 1.4. Probably\n"
65 " no good reason to change this unless you can retune to a good\n"
66 " benchmark for your data. Reasonable values are probably in the\n"
67 " range from 0.2 to 2.\n"
70 " Weight of an abstain vote. Default 1. So far, results do not\n"
71 " seem to be very sensitive to this parameter, but if you have\n"
72 " a good training set might be worth trying. Reasonable values\n"
73 " might range from 0.1 to 2.\n"
76 " Number of chunks to extract from the query sequence when searching\n"
77 " for parents. Default 4.\n"
80 " [Do not] use overlapping chunks. Default do not.\n"
83 " Minimum length of a chunk. Default 64.\n"
85 "--idsmoothwindow w\n"
86 " Length of id smoothing window. Default 32.\n"
89 " Minimum factional identity over smoothed window of candidate parent.\n"
93 " Maximum number of candidate parents to consider. Default 2. In tests so\n"
94 " far, increasing --maxp gives only a very small improvement in sensivity\n"
95 " but tends to increase the error rate quite a bit.\n"
99 " These options control how gapped columns affect counting of diffs.\n"
100 " If --skipgaps is specified, columns containing gaps do not found as diffs.\n"
101 " If --skipgaps2 is specified, if column is immediately adjacent to\n"
102 " a column containing a gap, it is not counted as a diff.\n"
103 " Default is --skipgaps --skipgaps2.\n"
107 " Minimum and maximum sequence length. Defaults 10, 10000.\n"
108 " Applies to both query and reference sequences.\n"
111 " Use local-X alignments. Default is global-X. On tests so far, global-X\n"
112 " is always better; this option is retained because it just might work\n"
113 " well on some future type of data.\n"
116 " Minimum fraction of the query sequence that must be covered by a local-X\n"
117 " alignment. Default 0.5. Applies only when --ucl is specified.\n"
120 " Do not display progress messages on stderr.\n"
123 " Write miscellaneous information to the log file. Mostly of interest\n"
124 " to me (the algorithm developer). Use --verbose to get more info.\n"
127 " In reference database mode, exclude a reference sequence if it has\n"
128 " the same label as the query. This is useful for benchmarking by using\n"
129 " the ref db as a query to test for false positives.\n"