UCHIME(1)

💖 UCHIME(1) — User Commands 💖

okay bestie, buckle up. This is the manual page for uchime, and we're gonna get through it together. No gatekeeping, no boring manpage voice, just facts with main character energy. 💅

✨ NAME ✨

uchime — reads a fasta file and reference file and outputs potentially chimeric sequences

🌸 DESCRIPTION 🌸

The chimera.uchime command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar.

💅 SYNOPSIS 💅

       uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime]

              [--uchimealns results.alns]

🎀 OPTIONS 🎀

• --input filename — Query sequences in FASTA format. If the --db option is not specified, uchime uses de novo detection. In de novo mode, relative abundance must be given by a string /ab=xxx/ somewhere in the label, where xxx is a floating-point number, e.g. >F00QGH67HG/ab=1.2/.
• --db filename — Reference database in FASTA format. Optional, if not specified uchime uses de novo mode.

WARNING ⚠️ The database is searched ONLY on the plus strand. You MUST include reverse-complemented sequences in the database if you want both strands to be searched.

• --abskew x — Minimum abundance skew. Default 1.9. De novo mode only. Abundance skew is:

min [ abund(parent1), abund(parent2) ] / abund(query).

• --uchimeout filename — Output in tabbed format with one record per query sequence. First field is score (h), second field is query label. For details, see manual.
• --uchimealns filename — Multiple alignments of query sequences to parents in humanreadable format. Alignments show columns with differences that support or contradict a chimeric model.
• --minh h — Minimum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease --xn, you may need to increase --minh, and vice versa.
• --mindiv div — Minimum divergence ratio, default 0.5. Div ratio is 100% - %identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase --mindiv to, say, 1.0 or 2.0, and also decrease --min h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.
• --xn beta — Weight of a no vote, also called the beta parameter. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.
• --dn n — Pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.
• --xa w — Weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2.
• --chunks n — Number of chunks to extract from the query sequence when searching for parents. Default 4.
• --[no]ovchunks — [Do not] use overlapping chunks. Default do not.
• --minchunk n — Minimum length of a chunk. Default 64.
• --idsmoothwindow w — Length of id smoothing window. Default 32.
• --minsmoothid f — Minimum factional identity over smoothed window of candidate parent. Default 0.95.
• --maxp n — Maximum number of candidate parents to consider. Default 2. In tests so far, increasing --maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit.
• --[no]skipgaps --[no]skipgaps2 — These options control how gapped columns affect counting of diffs. If --skipgaps is specified, columns containing gaps do not found as diffs. If --skipgaps2 is specified, if column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default is --skipgaps --skipgaps2.
• --minlen L --maxlen L — Minimum and maximum sequence length. Defaults 10, 10000. Applies to both query and reference sequences.
• --ucl — Use local-X alignments. Default is global-X. On tests so far, global-X is always better; this option is retained because it just might work well on some future type of data.
• --queryfract f — Minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5. Applies only when --ucl is specified.
• --quiet — Do not display progress messages on stderr.
• --log filename — Write miscellaneous information to the log file. Mostly of interest to me (the algorithm developer). Use --verbose to get more info.
• --self — In reference database mode, exclude a reference sequence if it has the same label as the query. This is useful for benchmarking by using the ref db as a query to test for false positives.

okay so now we enter the help section. Every option below has a description that is literally just help — unless I say otherwise. I'm keeping all of them, in order, because that's the rule. 🫶

• --abskew <float> — help
• --absort <str> — help
• --abx <float> — help
• --allpairs <str> — help
• --alpha <str> — help
• --band <uint> — help
• --blast6out <str> — help
• --[no]blast_termgaps — help
• --blastout <str> — help
• --bump <uint> — help
• --[no]cartoon_orfs — help
• --cc <str> — help
• --chain_evalue <float> — help
• --chain_targetfract <float> — help
• --chainhits <str> — help
• --chainout <str> — help
• --chunks <uint> — help
• --clstr2uc <str> — help
• --clump <str> — help
• --clump2fasta <str> — help
• --clumpfasta <str> — help
• --clumpout <str> — help
• --cluster <str> — help
• --compilerinfo — Write info about compiler types and #defines to stdout.
• --computekl <str> — help
• --db <str> — help
• --dbstep <uint> — help
• --[no]denovo — help
• --derep — help
• --diffchar <str> — help
• --dn <float> — help
• --doug <str> — help
• --droppct <uint> — help
• --evalue <float> — help
• --evalue_g <float> — help
• --exact — help
• --[no]fastalign — help
• --fastapairs <str> — help
• --fastq2fasta <str> — help
• --findorfs <str> — help
• --[no]flushuc — help
• --frame <int> — help
• --fspenalty <float> — help
• --gapext <str> — help
• --gapopen <str> — help
• --getseqs <str> — help
• --global — help
• --hash — help
• --hashsize <uint> — help
• --help — Display command-line options.
• --hireout <str> — help
• --hspalpha <str> — help
• --id <float> — help
• --idchar <str> — help
• --iddef <uint> — help
• --idprefix <uint> — help
• --ids <str> — help
• --idsmoothwindow <uint> — help
• --idsuffix <uint> — help
• --indexstats <str> — help
• --input <str> — help
• --[no]isort — help
• --k <uint> — help
• --ka_dbsize <float> — help
• --ka_gapped_k <float> — help
• --ka_gapped_lambda <float> — help
• --ka_ungapped_k <float> — help
• --ka_ungapped_lambda <float> — help
• --[no]label_ab — help
• --labels <str> — help
• --[no]leftjust — help
• --lext <float> — help
• --local — help
• --log <str> — Log file name.
• --[no]log_hothits — help
• --[no]log_query — help
• --[no]logmemgrows — help
• --logopts — Log options.
• --[no]logwordstats — help
• --lopen <float> — help
• --makeindex <str> — help
• --match <float> — help
• --matrix <str> — help
• --max2 <uint> — help
• --maxaccepts <uint> — help
• --maxclump <uint> — help
• --maxlen <uint> — help
• --maxovd <uint> — help
• --maxp <uint> — help
• --maxpoly <uint> — help
• --maxqgap <uint> — help
• --maxrejects <uint> — help
• --maxspan1 <uint> — help
• --maxspan2 <uint> — help
• --maxtargets <uint> — help
• --maxtgap <uint> — help
• --mcc <str> — help
• --mergeclumps <str> — help
• --mergesort <str> — help
• --minchunk <uint> — help
• --mincodons <uint> — help
• --mindiffs <uint> — help
• --mindiv <float> — help
• --minh <float> — help
• --minhsp <uint> — help
• --minlen <uint> — help
• --minorfcov <uint> — help
• --minspanratio1 <float> — help
• --minspanratio2 <float> — help
• --[no]minus_frames — help
• --mismatch <float> — help
• --mkctest <str> — help
• --[no]nb — help
• --optimal — help
• --orfstyle <uint> — help
• --otusort <str> — help
• --output <str> — help
• --[no]output_rejects — help
• --probmx <str> — help
• --query <str> — help
• --queryfract <float> — help
• --querylen <uint> — help
• --quiet — Turn off progress messages.
• --randseed <uint> — help
• --realign — help
• --[no]rev — help
• --[no]rightjust — help
• --rowlen <uint> — help
• --secs <uint> — help
• --seeds <str> — help
• --seedsout <str> — help
• --seedt1 <float> — help
• --seedt2 <float> — help
• --self — help
• --[no]selfid — help
• --simcl <str> — help
• --[no]skipgaps — help
• --[no]skipgaps2 — help
• --sort <str> — help
• --sortuc <str> — help
• --sparsedist <str> — help
• --sparsedistparams <str> — the docs literally just say help here 💀 that's the whole description, bestie, I'm not making it up
• --split <float> — also just says help 🫠
• --[no]ssort — yep, help again ✨
• --sspenalty <float> — help 💅
• --[no]stable_sort — help, she says 🎀
• --staralign <str> — help 🌸
• --stepwords <uint> — help 🦋
• --strand <str> — help 💖
• --targetfract <float> — help 😭
• --targetlen <uint> — help 💜
• --tmpdir <str> — help 🧚
• --[no]trace — help 🌈
• --tracestate <str> — help ⭐
• --[no]trunclabels — help 🍓
• --[no]twohit — help 🔥
• --uc <str> — help 👑
• --uc2clstr <str> — help 💀
• --uc2fasta <str> — help 🙈
• --uc2fastax <str> — help 🫶
• --uchime <str> — help ✨
• --uchimealns <str> — help 💅
• --uchimeout <str> — help 🎀
• --[no]ucl — help 🌸
• --uhire <str> — help 🦋
• --ungapped — help 💖
• --userfields <str> — help 😭
• --userout <str> — help 💜
• --usersort — help 🧚
• --uslink <str> — help 🌈
• --[no]usort — help ⭐
• --utax <str> — help 🍓
• --[no]verbose — help 🔥
• --version — shows the version and dips, that's it, that's the whole vibe 👑
• --w <uint> — help 💀
• --weak_evalue <float> — help 🙈
• --weak_id <float> — help 🫶
• --[no]wordcountreject — help ✨
• --[no]wordweight — help 💅
• --xa <float> — help 🎀
• --xdrop_g <float> — help 🌸
• --xdrop_nw <float> — help 🦋
• --xdrop_u <float> — help 💖
• --xdrop_ug <float> — help 😭
• --xframe <str> — help 💜
• --xlat — help 🧚
• --xn <float> — help 🌈

ngl bestie, a lot of these options are documented with nothing but the word help 😭 I'm not gatekeeping anything from you — that's genuinely all the original page says for them. Every flag, every argument type, every one of them is up there exactly as written. The mystery is part of the ✨lore✨.

👑 AUTHOR 👑

Robert C. Edgar

🔗 SEE ALSO 🔗

http://www.drive5.com/uchime

and that's the whole page, bestie!! 🫶 you made it to the end, main character behavior fr fr 💅 this was uchime v4.2.40, dated July 2013, living in the UCHIME(1) section of your manual — go forth and chimera-check something iconic, no cap 🌸✨🎀