/Metagenome_Assembly

Primary LanguageShell

Benchmarking de novo assembly methods on metagenomic sequencing data

Assemblers evaluated

Short-read assemblers

  • metaSPdes assembly_scripts/metaspades.sh <reads> <output>
  • MEGAHIT assembly_scripts/megahit.sh <reads> <output>

Linked-read assemblers

  • cloudSPAdes assembly_scripts/cloudspades.sh <reads> <output>
  • Athena assembly_scripts/athena.sh <short-read ssembly> <reads> <output>

Long-read assemblers

  • metaFlye assembly_scripts/metaflye.sh <reads> <output>
  • Canu assembly_scripts/canu.sh <reads> <output> <genome_size>
  • Lathe assembly_scripts/lathe.sh <long_reads> <short_reads> <output> <genome_size>
  • Shasta assembly_scripts/shasta.sh <reads> <output>
  • MECAT2 assembly_scripts/mecat2.sh <reads> <output> <genome_size>
  • NECAT assembly_scripts/necat.sh <reads> <output> <genome_size>
  • wtdbg2 assembly_scripts/wtdbg2.sh <reads> <output> <genome_size>

Hybrid assemblers

  • metaFlye-subassemblies assembly_scripts/metaflye-subassemblies.sh <short-read assembly> <long-read assembly> <output>
  • DBG2OLC assembly_scripts/dbg2olc.sh <short_reads> <long_reads> <output> <genome_size>
  • OPERA-MS assembly_scripts/opera-ms.sh <short_reads> <long_reads> <output>
  • OPERA-LG assembly_scripts/opera-lg.sh <short-read assembly> <short_reads> <long_reads> <output>

Time and memory

Time and memory consumed are measured by adding /usr/bin/time -v before the above commands.