ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

Abstract

Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. Results To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. Conclusions A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.

Infection cycle and phylogeny of the Polinton-like virus Phaeocystis globosa virus virophage-14T

“…Additional The terminal inverted repeats of the PgVV-14T were represented as separate fragments in the spades assembly and thus the following strategy was utilized. The PgVV scaffold was trimmed to include only the non-repeated region and extended with ContigExtender using the raw data 55 . The scaffold was trimmed to include a minimal region that would contain the fragments.…”

“…Long viral segments of at least 6000 bp were extracted by searching for MCP genes with the HMM profile for PLVs and viropages 9 and the NCLDV-specific profile VOG01840 from VOGDB (http://vogdb.org/). The extracted scaffolds were extended with Contig Extender v. 0.1 55 and then polished and gap-filled with pilon v. 1.24 74 . (46), Alveolata (11) and Haptophyta (10).…”

Large‐scale investigation of zoonotic viruses in the era of high‐throughput sequencing

“…56 Regarding the second issue, it is often challenging to obtain full-length viral genomes due to the low abundance of viral sequence reads in public HTS data (Box 1). Several approaches would be useful to obtain longer viral sequences: (i) developing more efficient sequencing assembly methods, 48,57 (ii) performing coassembly analysis using combined HTS data from samples considered to be infected with the same viruses, 58,59 or (iii) using long-read HTS data. 60 Second, it is difficult to accurately link virus-host relationships, even if viral sequences are identified in HTS data.…”

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

“…Metagenomic sequences can contain multiple species and sequence types. However, metagenomic assemblies from short reads (~100 to 300 bp) are usually fragmented due to presence of closely related strains, repeated sequences, and shared sequences between bacterial species ( 8 – 11 ). This fragmentation makes the identification of plasmid and bacteriophage DNA from assemblies challenging.…”