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README.md

skesa container

Strategic K-mer Extension for Scrupulous Assemblies

Main tool: skesa

Included tools and their respective versions:

  • skesa: 2.5.1
  • saute: 1.3.0
  • saute_prot: 1.3.0
  • gfa_connector: 1.1.1
  • kmercounter: 2.1.1

Code repository: https://github.com/ncbi/SKESA

Basic information on how to use this tool:

  • executable: skesa
  • help: -h
  • version: -v
  • description: Short read assembly

Full documentation: https://github.com/ncbi/SKESA

Example Usage

##  Assemble PE, interleaved reads in your $PWD
skesa --fastq /data/Ecoli-PE-interleaved.fastq.gz --use_paired_ends --cores 8 --contigs_out /data/Ecoli.skesa.contigs.fasta

## Example from SKESA readme, download K. pneumoniae reads from SRA and assemble
skesa --sra_run SRR1510963 --hash_count --contigs_out /data/SRR1510963_skesa.fasta

## example using PE reads that are in your PWD
skesa --cores 8 --memory 24 --reads /data/SRR11306390.sra_1.fastq /data/SRR11306390.sra_2.fastq --hash_count --contigs_out /data/SRR11306390.skesa.contigs.fasta