.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SKESA "1" "July 2019" "skesa 2.3.0" "User Commands"
.SH NAME
skesa \- strategic Kmer extension for scrupulous assemblies
.SH DESCRIPTION
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.
.SH OPTIONS
.SS "General options:"
.TP
\fB\-h\fR [ \fB\-\-help\fR ]
Produce help message
.TP
\fB\-v\fR [ \fB\-\-version\fR ]
Print version
.TP
\fB\-\-cores\fR arg (=0)
Number of cores to use (default all) [integer]
.TP
\fB\-\-memory\fR arg (=32)
Memory available (GB, only for sorted counter)
[integer]
.TP
\fB\-\-hash_count\fR
Use hash counter [flag]
.TP
\fB\-\-estimated_kmers\fR arg (=100)
Estimated number of unique kmers for bloom
filter (M, only for hash counter) [integer]
.TP
\fB\-\-skip_bloom_filter\fR
Don't do bloom filter; use \fB\-\-estimated_kmers\fR as
the hash table size (only for hash counter)
[flag]
.SS "Input/output options : at least one input providing reads for assembly must be specified:"
.TP
\fB\-\-fasta\fR arg
Input fasta file(s) (could be used multiple
times for different runs) [string]
.TP
\fB\-\-fastq\fR arg
Input fastq file(s) (could be used multiple
times for different runs) [string]
.TP
\fB\-\-use_paired_ends\fR
Indicates that a single (not comma separated)
fasta/fastq file contains paired reads [flag]
.TP
\fB\-\-sra_run\fR arg
Input sra run accession (could be used multiple
times for different runs) [string]
.TP
\fB\-\-contigs_out\fR arg
Output file for contigs (stdout if not
specified) [string]
.SS "Assembly options:"
.TP
\fB\-\-kmer\fR arg (=21)
Minimal kmer length for assembly [integer]
.TP
\fB\-\-min_count\fR arg
Minimal count for kmers retained for comparing
alternate choices [integer]
.TP
\fB\-\-max_kmer_count\fR arg
Minimum acceptable average count for estimating
the maximal kmer length in reads [integer]
.TP
\fB\-\-vector_percent\fR arg (=0.05)
Count for  vectors as a fraction of the read
number (1. disables) [float (0,1]]
.TP
\fB\-\-insert_size\fR arg
Expected insert size for paired reads (if not
provided, it will be estimated) [integer]
.TP
\fB\-\-steps\fR arg (=11)
Number of assembly iterations from minimal to
maximal kmer length in reads [integer]
.TP
\fB\-\-fraction\fR arg (=0.1)
Maximum noise to signal ratio acceptable for
extension [float [0,1)]
.TP
\fB\-\-max_snp_len\fR arg (=150)
Maximal snp length [integer]
.TP
\fB\-\-min_contig\fR arg (=200)
Minimal contig length reported in output
[integer]
.TP
\fB\-\-allow_snps\fR
Allow additional step for snp discovery [flag]
.SS "Debugging options:"
.TP
\fB\-\-force_single_ends\fR
Don't use paired\-end information [flag]
.TP
\fB\-\-seeds\fR arg
Input file with seeds [string]
.TP
\fB\-\-all\fR arg
Output fasta for each iteration [string]
.TP
\fB\-\-dbg_out\fR arg
Output kmer file [string]
.TP
\fB\-\-hist\fR arg
File for histogram [string]
.TP
\fB\-\-connected_reads\fR arg
File for connected paired reads [string]
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.