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.