KMERRESISTANCE(1)

💖 KMERRESISTANCE 💖

okay so bestie, welcome to the kmerresistance manual — it's a User Commands girlie through and through, and she's here to help you figure out which genes are hanging out in your WGS samples. no cap.

✨ NAME ✨

kmerresistance — correlates mapped genes with the predicted species of WGS samples. that's the whole vibe. 🦋

🌸 SYNOPSIS 🌸

ngl the original page leaves this section absolutely empty — not a single line, not even a crumb. so like, there's nothing to show you here, and I'm not gonna make stuff up. moving on bestie 💅

💜 DESCRIPTION 💜

KmerResistance correlates mapped genes with the predicted species of WGS samples — and the way that this this opens up so many doors?? It lets you identify genes in samples that have been poorly sequenced, and it gives you high accuracy predictions for samples with contamination. literally iconic behaviour.

KmerResistance has exactly one dependency, and it's KMA, which does the mapping for her. KMA is also freely available, so no gatekeeping here 🫶

🎀 OPTIONS 🎀

• -i — Input/query file name. REQUIRED, no skipping, periodt.
• -o — Output file. REQUIRED too bestie.
• -t_db — Template DB. REQUIRED.
• -s_db — Species DB. REQUIRED.
• -id — ID threshhold. default 70.0
• -dct — Depth correction threshhold. default 0.1
• -kma — alternative KMA. default kma

🌈 KMA options 🌈

these are the KMA settings, all up in here too:

• -i — Input/query file name. default None, REQUIRED
• -o — Output file. default None, REQUIRED
• -t_db — Template DB. default None, REQUIRED
• -k — Kmersize. default 16
• -e — evalue. default 0.05
• -delta — Align in pieces of delta. default 511
• -mem_mode — Use kmers to choose best template, and save memory. default False
• -ex_mode — Searh kmers exhaustively. default False
• -deCon — Remove contamination. default False
• -dense — Do not allow insertions in assembly. default False
• -ref_fsa — Consensus sequnce will have "n" instead of gaps. default False
• -matrix — Print assembly matrix. default False
• -mp — Minimum phred score. default 30
• -5p — Cut a constant number of nucleotides from the 5 prime. default 0
• -Sparse — Run KmerFinder. default False
• -ID — Minimum ID. default 1.0%
• -ss — Sparse sorting (q,c,d). default q
• -shm — Use shared DB made by kma_shm. default 0 (lvl)
• -swap — Swap DB to disk. default 0 (lvl)
• -1t1 — Skip HMM. default False
• -boot — Bootstrap sequence. default False
• -mrs — Minimum alignment score, normalized to alignment length. default 0.5
• -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
• -h — Shows this help message. she's helpful like that 💖

🧚 EXAMPLES 🧚

Mapping reads against resistance genes — this is the moment, bestie:

kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria

look at her go 😭✨

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. we love a generous king 💜

okay so this is kmerresistance version 2.0+git20180205...., dated June 2018, and yeah — that's the whole KMERRESISTANCE(1) page. slay, go map some genes, ily bye 🎀💅🦋