MAPSEMBLER2_KISSREADS(1)

💖 MAPSEMBLER2_KISSREADS(1) 💖

okay bestie, welcome to mapsembler2_kissreads, a User Commands classic 🫶 — this is the manual page for it and we're gonna go through everything, no skips, periodt.

✨ NAME ✨

mapsembler2_kissreads — checks, for each sequence contained into the toCheck.fasta, if it is read coherent with reads from readsA.fasta or readsB.fasta 🦋

🌸 SYNOPSIS 🌸

mapsembler2_kissreads <toCheck.fasta> <readsC1.fasta> [<readsC2.fasta>
[<readsC3.fasta] ...] [-k value] [-c value] [-d value] [-O value] [-o
name] [-u name] [-n] [-I] [-i index_stride] [-m align_file] [-s] [-f]
[-h]

like, yes, that's a lot of brackets, but you got this 💅

🎀 DESCRIPTION 🎀

So here's the vibe: for each sequence contained into the toCheck.fasta, it checks if it is read coherent — meaning each position is covered by at least "min_coverage" read(s) — with reads from readsA.fasta or readsB.fasta. A sequence s from toCheck gets treated as follows:

• if s is coherent with at least one read set: output the sequence as follows

>original fasta
comment|C1:min<avg-corr_avg<max|C2:min<avg-cor_avg<max|C3...: >s

With A:min<avg-cor_avg<max standing for: value of the position having minimal coverage in readsA.fasta < average coverage in readsA.fasta - R-squarred corrected average in readsA.fa < value of the position having maximal coverage in readsA.fasta. The coverage is the number of reads that perfectly mapped a position. 👑

• Any other situation (s not coherent with any): couple non read coherent, not outputed 🙈

💅 OPTIONS 💅

• -k size_seed — will use seeds of length size_seed. Default: 25.
• -O minimal_read_overlap — a read can be mapped if its overlap is a least "minimal_read_overlap". Default: k
• -c min_coverage — a sequence is covered by at least min_coverage coherent reads. Default: 2
• -d max_substitutions — maximal number of substitutions authorized between a read and a fragment. Note that no substitution is allowed on the central position while anaylizing the kissnp output. Default: 1.
• -o file_name — write read-coherent outputs. Default: standard output
• -u file_name — write unread-coherent outputs. Default: standard output
• -n — the input file (toCheck.fasta) is a kissnp output (incompatible with -I option)

in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no substitution is authorized on this position.

• -I — the input file (toCheck.fasta) is an Intl output (incompatible with -n option)
• -i index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no heuristic)
• -t max — number of threads (also limited by number of input files)
• -m align_file — write a file of reads mapped to sequences in file align_file
• -s — silent mode 🤫
• -f — outputs coherent events in a standard fasta file format
• -h — prints this message and exit

ngl bestie, watch out for -n and -I — they are incompatible with each other, so don't try to run both at once, it's giving chaos 😭

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

and that's the whole thing, bestie 🌈 fr fr you now know mapsembler2_kissreads better than it knows itself. this was mapsembler2_kissreads version 2.2.4, dated October 2018 — mwah, slay, bye 💜✨🎀