Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity
biorxiv(2023)
Abstract
Despite long-read sequencing enables to generate complete genomes of unculturable microbes, its high cost hinders its widespread application in large cohorts. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. We developed Pangaea to improve metagenome assembly using short-reads with physical or virtual barcodes. It adopts a deep-learning-based binning algorithm to assemble the co-barcoded reads with similar sequence contexts and abundances to improve assemblies of high- and medium-abundance microbes. Pangaea also leverages a multi-thresholding reassembly strategy to refine assembly for low-abundance microbes. We benchmarked Pangaea with linked-reads and a combination of short- and long-reads from mock communities and human gut metagenomes. Pangaea achieved significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea was also observed to generate three complete and circular NCMAGs on the human gut microbiomes.
### Competing Interest Statement
LJH is an employee of Kangmeihuada GeneTech Co., Ltd (KMHD).
* MAG
: Metagenome-Assembled Genome
NCMAG
: Near-Complete Metagenome-Assembled Genome
OGRE
: Overlap Graph-based Read clustEring
PacBio CLR
: PacBio Continuous Long-Reads
RSS
: Resident Set Size
rRNA
: Ribosomal RNA
stLFR
: single-tube Long Fragment Read
TELL-Seq
: Transposase Enzyme-Linked Long-read Sequencing
TNF
: TetraNucleotide Frequency
tRNA
: Transfer RNA
UST
: Universal Sequencing Technology
VAE
: Variational AutoEncoder
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