COPE (for Joining PE Reads) and Arapan-S (for Small Genomes)

COPE (for Joining PE Reads) and Arapan-S (for Small Genomes)

Two new papers may interest our readers. The first one from BGI will come out in Bioinformatics and it joins PE reads before performing genome assembly using de Bruijn assembler. The second one is on performing highly accurate assembly of small genomes.

Many groups are realizing that it is a waste to discard information provided by paired end reads, and the solutions developed by them fall into two tags: [] categories -

(a) some kind of pre-processing module to join those reads that can be joined and continuing with the assembly,

(b) modification of de Bruijn graph formalism to incorporate pairing information.

The first category is great, when it works. However, it may not be useful, when the insert length large compared to read length. SPAdes (and possibly Monument assembler of Rayan Chikhi) fall into the second category, whereas FLASH, COPE and a poster mentioned here previously use method in the first category.

**COPE: An accurate k-mer based pair-end reads connection tool

to facilitate genome assembly**

B. Liu et al.

Result: In this paper, we present an efficient tool called COPE (Connecting Overlapped Pair-End reads), to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30x simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is respectively 10% and 2% higher than the most recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14 fold improvement in the N50 measurement when compared to the contigs produced using unconnected reads.

Source code can be downloaded from here.


Arapan-S comes from a Japanese group and it claims to assemble very small genomes at great accuracy. We do not know, where it stands compared to Ray.

**Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes


Mohammed Sahli1* and Tetsuo Shibuya


Our findings show that the accuracy of the assembly was very high; the result was checked against the European Bioinformatics Institute (EBI) database using the NCBI BLAST Sequence Similarity Search. The identity and the genome coverage was more than 99%. We also compared the efficiency of Arapan-S with other well-known assemblers. In dealing with small genomes, the accuracy of Arapan-S is significantly higher than the accuracy of other assemblers. The assembly process is very fast and requires only a few seconds.

Project home page is here.

Written by M. //