SEGEMEHL(1)

💖 SEGEMEHL(1) 💖

okay bestie, welcome to the segemehl manual page, living in the User Commands section, and honestly? she's a whole legend. let's get into it 🧚✨

---

🌸 NAME 🌸

segemehl — Heuristic mapping of short sequences. that's it, that's the vibe. no cap. 💅

---

✨ SYNOPSIS ✨

like, here's how you actually call her:

segemehl [-besVOc] -d <file> [<file>] [-q <file>] [-p <file>] [-i
<file>] [-j <file>] [-x <file>] [-y <file>] [-G <file>] [-g <string>]
[-t <n>] [-o <string>] [-u <file>] [-B <string>] [-F <n>] [-S
[<basename>]] [-A <n>] [-D <n>] [-E <double>] [-H] [-m <n>] [-Z <n>] [-W
<n>] [-U <n>] [-l <f>] [-w <double>] [-X <n>] [-J <n>] [-I <n>] [-M <n>]
[-n <n>] [-r <n>] [--skipidcheck] [--showalign] [--nohead]

look at all those flags, she's booked and busy 🎀

---

🦋 DESCRIPTION 🦋

so. Segemehl is a software to map short sequencer reads to reference genomes. she implements a matching strategy based on enhanced suffix arrays (ESA). she accepts fasta and fastq queries (gzip’ed and bgzip'ed, because she's inclusive like that 💅). and like — not only does she align reads from standard DNA- and RNA-seq protocols, she ALSO lets you map bisulfite converted reads (Lister and Cokus) and she implements a split read mapping strategy. multi-talented queen, honestly. 👑

her output is a SAM or BAM formatted alignment file. and in the case of split-read mapping, extra BED files get written to the disc — those BED files may be summarized with the postprocessing tool haarz. and for bisulfite converted reads? raw methylation rates may also be called with haarz. she works with haarz, iconic duo, iykyk. 🫶

in brief bestie — here's the tea ☕

so, for each suffix of a read, segemehl aims to find the best-scoring seed. seeds might contain insertions, deletions, and mismatches (differences). the number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program — like, actually important, don't skip this. subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. and finally, reads with a minimum accuracy of percent are reported to the user. periodt. 💖

---

👑 OPTIONS 👑

🍓 INPUT 🍓

• -d, --database <file> [<file>] — list of path/filename(s) of fasta database sequence(s). yes, plural, you can hand her a whole list 💅
• -q, --query <file> — path/filename of query sequences (default:none)
• -p, --mate <file> — path/filename of mate pair sequences (default:none)
• -i, --index <file> — path/filename of db index (default:none)
• -j, --index2 <file> — path/filename of second db index (default:none)
• -x, --generate <file> — generate db index and store to disk (default:none)
• -y, --generate2 <file> — generate second db index and store to disk (default:none)
• -G, --readgroupfile <file> — filename to read @RG header (default:none)
• -g, --readgroupid <string> — read group id (default:none)
• -t, --threads <n> — start <n> threads (default:1). give her more threads, she'll go faster, she deserves it 🏃‍♀️💨

---

🌈 OUTPUT 🌈

• -o, --outfile <string> — outputfile (default:none)
• -b, --bamabafixoida — generate a bam output (-o <filename> required). yes that's the actual flag name, we don't question it, we just respect it 🙈
• -u, --nomatchfilename <file> — filename for unmatched reads (default:none)
• -e, --briefcigar — brief cigar string (M vs X and =)
• -s, --progressbar — show a progress bar. honestly the most soothing option on this whole page, watching her work 😭💖
• -B, --filebins <string> — file bins with basename <string> for easier data handling (default:none)
• -V, --MEOP — output MEOP field for easier variance calling in SAM (XE:Z:)

---

🌸 ALIGNMENT 🌸

• -F, --bisulfite <n> — bisulfite aln with methylC-seq/Lister et al. (=1) or bs-seq/Cokus et al. protocol (=2) (default:0)
• -S, --splits [<basename>] — detect split/spliced reads. (default:none)
• -A, --accuracy <n> — min percentage of matches per read in semi-global alignment (default:90)
• -D, --differences <n> — search seeds initially with <n> differences (default:1)
• -E, --evalue <double> — max evalue (default:5.000000)
• -H, --hitstrategy — report only best scoring hits (=1) or all (=0) (default:1)
• -m, --minsize <n> — minimum length of queries (default:12)
• -Z, --minfraglen <n> — min length of a spliced fragment (default:20)
• -W, --minsplicecover <n> — min coverage for spliced transcripts (default:80)
• -U, --minfragscore <n> — min score of a spliced fragment (default:18)
• -l, --splicescorescale <f> — report spliced alignment with score s only if <f>*s is larger than next best spliced alignment (default:0.900000)
• -w, --maxsplitevalue <double> — max evalue for splits (default:50.000000)

---

💜 SPECIAL 💜

• -X, --dropoff <n> — dropoff parameter for extension (default:8)
• -J, --jump <n> — search seeds with jump size <n> (0=automatic) (default:0)
• -O, --order — sorts the output by chromsome and position (might take a while!). bestie she warned you, don't be surprised when it takes a while 😭
• -I, --maxpairinsertsize <n> — maximum size of the inserts (paired end) in case of multiple hits (default:200000)
• -M, --maxinterval <n> — maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than <n> times (default:100)
• -c, --checkidx — check index
• -n, --extensionpenalty <n> — penalty for a mismatch during extension (default:4)
• -r, --maxout <n> — maximum number of alignments that will be reported. If set to zero, all alignments will be reported (default:0)
• --skipidcheck — do not check whether the fastq ids of mates / paired ends match. Instead, the first mate (-q) will be used for output only.
• --showalign — show alignments
• --nohead — do not output header

---

💀 BUGS 💀

found a bug? not her fault, but also please tell her 🥺 — Please report bugs to steve@bioinf.uni-leipzig.de

---

🎀 SEE ALSO 🎀

• http://www.bioinf.uni-leipzig.de/Software/segemehl/

go look, she has a whole website, main character energy fr fr ✨

---

📚 REFERENCES 📚

• 2008 Bioinformatik Leipzig
• 2018 Leibniz Institute on Aging (FLI)

---

🫶 AUTHOR 🫶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, you ate 💅✨

---

okay that's the whole page bestie, you're officially segemehl-literate, go map some reads 🌸🦋💖

segemehl 0.3 — October 2018 — SEGEMEHL(1) 💜 mwah, go slay 👑