Performance of Genome Assemblers

In this study six assemblers, i.e. Velvet, SOAPdenovo, Edina, Euler, AbySS and SSAKE (all having the ability to assemble Illumina’s short reads) have been evaluated. All these assemblers were evaluated on one real and four hypothetical genomes. Detail result and explanation is given in paper, here we are providing few important comparisons. Each assembler have been evaluated using single end reads and paired end reads.

Assemblers evaluated in this study

Velvet 1.0.12

SOAPdenovo 1.04

SOAPdenovo 1.03

Euler-sr 1.1.2

Edena 2.1.1

SSAKE 3.4

SSAKE 3.5

AbySS 1.2.4

Benchmarking results

Single end assembly

Genome A	Graph 1	Graph 2	Graph 3	Data
Genome B	Graph 1	Graph 2	Graph 3	Data
Genome C	Graph 1	Graph 2	Graph 3	Data
Genome D	Graph 1	Graph 2	Graph 3	Data
Genome R	Graph 1	Graph 2	Graph 3	Data

Paired end assembly 1

Genome A	Graph 1	Graph 2	Graph 3	Data
Genome B	Graph 1	Graph 2	Graph 3	Data
Genome C	Graph 1	Graph 2	Graph 3	Data
Genome D	Graph 1	Graph 2	Graph 3	Data
Genome R	Graph 1	Graph 2	Graph 3	Data

Graph 1: Graph between Hash length (K) and N 50 Contig length.
Graph 2: Graph between Hash length (K) and Error rate(%) of the total assembly.
Graph 3: Graph between N 50 Contig length and Error rate(%) of the total assembly.