KMER-MASK(1)

💖 KMER-MASK(1) 💖

okay bestie, sit down, hydrate, because we're reading the kmer-mask manual page — it's a User Commands page (section 1, she's a command, she's booked and busy) and honestly? she eats. no cap. 🫶

✨ NAME ✨

kmer-mask — mask and filter set of nucleotide sequences by kmer content 💅

🌸 SYNOPSIS 🌸

kmer-mask {-novel|-confirmed} [-mdb mer-database] [-ms mer-size] [-edb exist-database] [-m min-size] [-e extend-size] [-lowthreshold l] [-highthreshold h] [-t threads] [-v] [-h histogram] [-promote|-demote|-discard] -1 in.1.fastq [-2 in.2.fastq] -o output-prefix

🦋 DESCRIPTION 🦋

Mask and filter set of sequences (presumed to be reads) by kmer content. Masking can be done to retain novel sequence not in the database, or to retain confirmed sequence present in the database. Filtering will segregate sequences fully, partially or not masked. it's giving sorting-hat energy fr fr 🎀

💅 OPTIONS 💅

• -mdb mer-database — load masking kmers from meryl(1) mer-database 🌈
• -ms mer-size — bestie the original page just… doesn't describe this one. she's mysterious. she's mer-size. we respect her privacy 💀
• -edb exist-database — save masking kmers to an existDB(1) file exist-database for faster restarts 🔥
• -1 in.1.fastq — the first input reads file (her description is chilling with -2 right below, iykyk)
• -2 in.2.fastq — input reads files in fastq, fastq.gz, fastq.bz2 or fastq.xz format. The second is optional, but messes up the output classification if not present. ⚠️
• -o out — prefix for output reads ✨
  • out.fullymasked.[12].fastq — reads with below lowthreshold bases retained
  • out.partiallymasked.[12].fastq — reads in between
  • out.retained.[12].fastq — reads with more than hightreshold bases retained
  • out.discarded.[12].fastq — reads with conflicting status
• -m min-size — ignore database hits below this many consecutive kmers (0)
• -e extend-size — extend database hits across this many missing kmers (0)
• -novel — RETAIN novel sequence not present in the database 👑
• -confirmed — RETAIN confirmed sequence present in the database 👑
• -promote — promote the lesser RETAINED read to the status of the more RETAINED read, read1=fullymasked and read2=partiallymasked -> both are partiallymasked
• -demote — demote the more RETAINED read to the status of the lesser RETAINED read, read1=fullymasked and read2=partiallymasked -> both are fullymasked
• -discard — discard pairs with conflicting status (DEFAULT), read1=fullymasked and read2=partiallymasked -> both are discarded

📊 stats on stderr, number of sequences with amount RETAINED 📊

• -lowthreshold t — (0.3333)
• -highthreshold t — (0.6667)
• -h histogram — write a histogram of the amount of sequence RETAINED
• -t t — use t compute threads 🧵
• -v — show progress 🐣

🔭 SEE ALSO 🔭

• meryl(1)
• existDB(1)

not me being emotionally attached to a kmer masker. the way that -promote, -demote and -discard decide the fate of a conflicted read pair is main character energy and honestly iconic 🎀

okay so that's the whole page, bestie — this is kmer-mask version 0~20150520+2004, dated May 2015, and she's still slaying 💖✨🦋🌸💅