SURANKCO-FEATURE(1)

💖 SURANKCO-FEATURE 💖

okay bestie, gather round, because this is the manual page for surankco-feature, and it lives in the User Commands section of the manual. yes, THE User Commands section. iconic behavior only.

✨ NAME ✨

surankco-feature — feature generation from contigs and corresponding reads 🧬🌸

🦋 SYNOPSIS 🦋

surankco-feature [options]

that's it. that's the whole vibe. just options, no positional drama. we love a low-maintenance queen. 💅

🌸 DESCRIPTION 🌸

So like, what does this do? Feature generation, obviously. From contigs — which need to be in ACE format — and the corresponding reads, which you're gonna bring in QUAL or FASTQ format. that's the whole assignment. contigs plus reads, features come out. periodt. ✨

🎀 OPTIONS 🎀

okay this is the part where you actually pay attention, bestie, because every single flag matters and I'm not about to let you skim. 🙈

• -a ASSEMBLIES, --assemblies=ASSEMBLIES — hand over a list of assembly files, comma separated, and the suffixes HAVE to be correct, no cap. like ".ace" — mandatory, fr fr. 💀
• -d DIRECTORY, --directory=DIRECTORY — point at a directory that's holding assembly files in the format you declared (default is ace, go peek at -f if you forgot).
• -f ASSEMBLY.FORMAT, --assembly.format=ASSEMBLY.FORMAT — tell it the assembly/contig format, aka the suffix. your choices are "ace" (the default, she's the main character) or "contigs.fasta".
• -r READ.QUALITY.FORMAT, --read.quality.format=READ.QUALITY.FORMAT — declare the read quality format: qual, qua or fastq for ACE (default is "qual"), and resp. sam or bam for contigs.fasta (default is "sam"). pick your fighter. 🥊
• -q FASTQ.VERSION, --fastq.version=FASTQ.VERSION — set the fastq version: auto, sanger, solexa, illumina13, illumina15, illumina18 (that last one is the default, she's the chosen one). only needed for ACE assemblies, so if you're not in ACE land you can skip. 🫶
• -s SPLIT.REGEX, --split.regex=SPLIT.REGEX — drop a regular expression to cutoff read names, which you'd need if the assembler went and modified them. only needed for ACE assemblies. ⚠️ and listen closely: if you need a backslash "\", you have to write "\\\\"! yes really. the escaping is giving chaos but that's the rule. 😭
• -t THREADS, --threads=THREADS — how many cores or threads you wanna throw at it. might speed up some parallelized operations (default: 1). go on, give her more, she can handle it.
• -m MEMORY, --memory=MEMORY — the maximum memory usage, in Gb, for Java's virtual machine (default: 32). if you're working with big data sets and it starts reporting heap space problems, try bumping this up. 🔥
• -k, --kmer.features — decides whether k-mer features get computed or not. heads up: this is experimental and has a very long runtime. the default is not to do it, and honestly? respect the default. 💀
• -g EXPECTED.GENOME.SIZE, --expected.genome.size=EXPECTED.GENOME.SIZE — give a list of expected genome sizes (comma separated) or just one value that applies to all assemblies. default is 0, which makes it estimate the genome sizes as the sum of contig lengths. she'll figure it out herself, queen. 👑
• -c CONTIG.SIZE.FILTER, --contig.size.filter=CONTIG.SIZE.FILTER — set a minimum contig size. default: 0.
• -h, --help — show this help message and exit. the classic. the icon. 🌈

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. shoutout to Andreas for real, that's generous energy and we love to see it. 🫶

and that's the whole page, bestie! 🎀 this was surankco-feature version 0.0.r5, dated March 2016 — old enough to have a driver's license but still serving. mwah. 💖✨🦋