KMA(1)

💖 KMA(1) 💖

User Commands · kma · bestie edition ✨

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🌸 NAME 🌸

kma — maps and/or aligns raw reads to a template database 🧬✨

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🦋 DESCRIPTION 🦋

okay so. KMA-1.3.23 maps and/or aligns raw reads to a template database. that's the whole vibe. it's giving aligner, it's giving mapper, it's giving main character energy 💅

Every option below comes with its Desc (what it does) and its Default (what it does if you say nothing, which is very demure, very mindful of it). scroll, bestie, there's a lot 👑

🎀 Input 🎀

• -i — single end input(s). Default: stdin 📥
• -ipe — paired end input(s) 👯
• -int — interleaved input(s) 🌀

🌈 Output 🌈

• -o — output prefix 🏷️
• -ef — output additional features. Default: False
• -vcf — output vcf file, 2 to apply FT. Default: False
• -sam — output sam, 4/2096 for mapped/aligned. Default: False
• -nc — no consensus file. Default: False
• -nc — no aln file. Default: False
• -nf — no frag file. Default: False
• -matrix — output assembly matrix. Default: False
• -a — output all template mappings. Default: False
• -and — use both mrs and p-value on consensus. Default: or
• -oa — use neither mrs or p-value on consensus. Default: False

ngl bestie, -nc really does show up twice in the list — once for the consensus file, once for the aln file. it's iconic, it's a two-for-one, we don't question it 🙈

🍓 Consensus 🍓

• -bc — minimum support to call bases. Default: 0
• -bcNano — altered indel calling for ONT data. Default: False
• -bcd — minimum depth to cal bases. Default: 1
• -bcg — maintain insignificant gaps. Default: False
• -ID — minimum consensus ID. Default: 1.0%
• -dense — skip insertion in consensus. Default: False
• -ref_fsa — use n's on indels. Default: False

✨ General ✨

• -t_db — template DB 🗄️
• -p — p-value. Default: 0.05
• -shm — use DB in shared memory. Default: 0
• -mmap — memory map *.comp.b. Default: False
• -tmp — set directory for temporary files 📁
• -t — number of threads. Default: 1 🧵
• -status — extra status. Default: False
• -verbose — extra verbose. Default: False 🗣️
• -c — citation 📜
• -v — version
• -h — shows this help message 🆘

👑 Template mapping 👑

• -ConClave — ConClave version. Default: 1
• -mem_mode — base ConClave on template mappings. Default: False
• -proxi — proximity scoring (negative for soft). Default: False/1.0
• -ex_mode — searh kmers exhaustively. Default: False
• -deCon — remove contamination. Default: False 🧼
• -Sparse — only count kmers. Default: False
• -ss — sparse sorting (q,c,d). Default: q
• -Mt1 — map everything to one template. Default: False/0
• -pm — pairing method (p,u,f). Default: u
• -1t1 — one query to one template. Default: False
• -hmm — use a HMM to assign template(s). Default: True
• -ck — count k-mers over pseudo alignment. Default: False

🧚 Chaining 🧚

• -k — k-mersize. Default: DB defined
• -ts — trim front of seeds. Default: 0
• -ssa — seeds soround alignments. Default: False
• -ex_mode — searh kmers exhaustively. Default: False
• -fpm — pairing method (p,u,f). Default: u
• -mq — minimum mapping quality. Default: 0

yes, -ex_mode said what it said up in Template mapping and it's saying it again here. consistent queen 💅

💜 Alignment 💜

• -ca — circular alignments. Default: False 🔄
• -mrs — minimum relative alignment score. Default: 0.5
• -mrc — minimum query coverage. Default: 0.0
• -ml — minimum alignment length. Default: 16
• -reward — score for match. Default: 1
• -penalty — penalty for mismatch. Default: 2
• -gapopen — penalty for gap opening. Default: 3
• -gapextend — penalty for gap extension. Default: 1
• -per — reward for pairing reads. Default: 7
• -Npenalty — penalty matching N. Default: 0
• -transition — penalty for transition. Default: 2
• -transversion — penalty for transversion. Default: 2
• -sasm — skip alignment. Default: False

🎀 Trimming 🎀

• -mp — minimum phred score. Default: 20 ✂️
• -eq — minimum avg. quality score. Default: 0
• -5p — trim 5 prime. Default: 0
• -3p — trim 3 prime. Default: 0
• -ml — minimum length. Default: 16
• -xl — maximum length on se. Default: 2147483647
• -boot — bootstrap sub-sequence. Default: False

and yes again — -ml pulls double duty. 16 for minimum alignment length upstairs, 16 for minimum length right here. same name, different department, both slaying 😭

🌟 Presets 🌟

• -apm — sets both pm and fpm. Default: u
• -cge — set CGE penalties and rewards. Default: False
• -mint2 — set 2ng gen Mintyper preset. Default: False
• -mint3 — set 3rd gen Mintyper preset. Default: False

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🫶 AUTHOR 🫶

this manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. king behavior honestly 👑

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kma 1.3.23 · July 2021 · that's the whole page bestie, thanks for reading, go map some reads 💖✨🦋🎀