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SKESA(1) User Commands SKESA(1)

skesa - strategic Kmer extension for scrupulous assemblies

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources. SKESA has been used for assembling over 272,000 read sets in the Sequence Read Archive at NCBI and for real-time pathogen detection.

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Number of cores to use (default all) [integer]
Memory available (GB, only for sorted counter) [integer]
Use hash counter [flag]
Estimated number of unique kmers for bloom filter (M, only for hash counter) [integer]
Don't do bloom filter; use --estimated_kmers as the hash table size (only for hash counter) [flag]

Input fasta file(s) (could be used multiple times for different runs) [string]
Input fastq file(s) (could be used multiple times for different runs) [string]
Indicates that a single (not comma separated) fasta/fastq file contains paired reads [flag]
Input sra run accession (could be used multiple times for different runs) [string]
Output file for contigs (stdout if not specified) [string]

Minimal kmer length for assembly [integer]
Minimal count for kmers retained for comparing alternate choices [integer]
Minimum acceptable average count for estimating the maximal kmer length in reads [integer]
Count for vectors as a fraction of the read number (1. disables) [float (0,1]]
Expected insert size for paired reads (if not provided, it will be estimated) [integer]
Number of assembly iterations from minimal to maximal kmer length in reads [integer]
Maximum noise to signal ratio acceptable for extension [float [0,1)]
Maximal snp length [integer]
Minimal contig length reported in output [integer]
Allow additional step for snp discovery [flag]

Don't use paired-end information [flag]
Input file with seeds [string]
Output fasta for each iteration [string]
Output kmer file [string]
File for histogram [string]
File for connected paired reads [string]

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

July 2019 skesa 2.3.0