NAME

       skesa - strategic Kmer extension for scrupulous assemblies

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.

OPTIONS

   General options:
       -h [ --help ]
              Produce help message

       -v [ --version ]
              Print version

       --cores arg (=0)
              Number of cores to use (default all) [integer]

       --memory arg (=32)
              Memory available (GB, only for sorted counter) [integer]

       --hash_count
              Use hash counter [flag]

       --estimated_kmers arg (=100)
              Estimated  number  of  unique  kmers  for  bloom  filter (M, only for hash counter)
              [integer]

       --skip_bloom_filter
              Don't do bloom filter; use --estimated_kmers as the hash table size (only for  hash
              counter) [flag]

   Input/output options : at least one input providing reads for assembly must be specified:
       --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 (stdout if not specified) [string]

   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) [float (0,1]]

       --insert_size arg
              Expected  insert  size  for  paired  reads  (if not provided, it will be estimated)
              [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 additional step for snp discovery [flag]

   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]

AUTHOR

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