Assemblers

Short Read / Illumina

ABySS https://github.com/bcgsc/abyss - de novo assembler for short, paired end reads and large genome

Velvet - old and less supported

Trinity

SOAPdenovo2 -

Meraculous

PERGA -

PE-Assembler

Forge

Long Read / Nanopore / PacBio

nanopore.exact.fasta contains a collection of reads randomly extracted from a 5mb section of hg38.

Canu

Canu

canu -p SEQUENCE_PREFIX -d OUT_DIRECTORY genomeSize=5m useGrid=false -corrected -trimmed -nanopore nanopore.exact.fasta

Frye

Frye

flye --genome-size 5m --threads 8 --nano-cor nanopore.exact.fasta --out-dir OUT_DIRECTORY

Shasta

Shasta

shasta --input nanopore.exact.fasta --assemblyDirectory OUT_DIRECTORY

Raven

Raven

Testing and Comparison

Read Simulator was created to generate reads to test assemblers by randomly selecting subsections of a reference.