SKESA(1)

💖 SKESA — the manual page, but make it a group chat 💖

okay bestie, sit DOWN, because this is skesa(1) from the User Commands part of the manual and it's genuinely iconic. 🧚✨

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🌸 NAME 🌸

skesa — strategic kmer extension for scrupulous assemblies

no cap, that's the whole name. it's giving acronym main character energy. 💅

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✨ DESCRIPTION ✨

SKESA is a DeBruijn graph-based de-novo assembler, and it was literally designed to assemble reads of microbial genomes that were sequenced using Illumina. 🦋

so like, when you compare it to SPAdes and MegaHit? SKESA produces assemblies that have:

• high sequence quality 👑
• high contiguity 💫
• it handles low-level contamination in reads (yes, it's unbothered 💅)
• it is fast 🔥
• and it produces an identical assembly for the same input when you assemble multiple times with the same or different compute resources

that last one? reproducibility queen. periodt.

and the receipts, because she's not just pretty: SKESA has been used for assembling over 272,000 read sets in the Sequence Read Archive at NCBI, and for real-time pathogen detection. not me being deployed in an actual public health emergency 😭 iconic behavior.

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🎀 OPTIONS 🎀

🫶 General options:

• -h [ --help ] — produces the help message, aka the "bestie explain" button
• -v [ --version ] — prints the version
• --cores arg (=0) — number of cores to use (default is all of them, she's greedy in a cute way) [integer]
• --memory arg (=32) — memory available (in GB, only for sorted counter) [integer]
• --hash_count — use the hash counter [flag]
• --estimated_kmers arg (=100) — estimated number of unique kmers for the bloom filter (in M, only for hash counter) [integer]
• --skip_bloom_filter — don't do the bloom filter; use --estimated_kmers as the hash table size instead (only for hash counter) [flag]

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🌈 Input/output options: at least one input providing reads for assembly must be specified:

bestie this is not optional. you literally have to give her reads. at least one. 💀

• --fasta arg — input fasta file(s) (could be used multiple times for different runs) [string]
• --fastq arg — input fastq file(s) (could be used multiple times for different runs) [string]
• --use_paired_ends — indicates that a single (not comma separated) fasta/fastq file contains paired reads [flag]
• --sra_run arg — input sra run accession (could be used multiple times for different runs) [string]
• --contigs_out arg — output file for contigs (goes to stdout if not specified) [string]

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🧬 Assembly options:

• --kmer arg (=21) — minimal kmer length for assembly [integer]
• --min_count arg — minimal count for kmers retained for comparing alternate choices [integer]
• --max_kmer_count arg — minimum acceptable average count for estimating the maximal kmer length in reads [integer]
• --vector_percent arg (=0.05) — count for vectors as a fraction of the read number (1. disables it) [float (0,1]]
• --insert_size arg — expected insert size for paired reads (if you don't provide it, it will be estimated, she'll figure it out 🫶) [integer]
• --steps arg (=11) — number of assembly iterations from minimal to maximal kmer length in reads [integer]
• --fraction arg (=0.1) — maximum noise to signal ratio acceptable for extension [float [0,1)]
• --max_snp_len arg (=150) — maximal snp length [integer]
• --min_contig arg (=200) — minimal contig length reported in output [integer]
• --allow_snps — allow an additional step for snp discovery [flag]

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🙈 Debugging options:

• --force_single_ends — don't use paired-end information [flag]
• --seeds arg — input file with seeds [string]
• --all arg — output fasta for each iteration [string]
• --dbg_out arg — output kmer file [string]
• --hist arg — file for histogram [string]
• --connected_reads arg — file for connected paired reads [string]

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💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout Andreas, absolute legend, ate and left no crumbs. 🎀

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okay and the cute sign-off: this whole thing is for skesa 2.3.0, dated July 2019, filed under SKESA(1). go assemble something slay, bestie. 💖✨🦋