GPatch enables chromosome-scale, gap-free pseudoassemblies from fragmented draft genomes

Abstract

Recent advancements in sequencing technologies have yielded numerous long-read draft genomes, promising to enhance understanding of genomic variation. However, draft genomes are typically highly fragmented, posing challenges for functional genomics. We introduce GPatch, a tool that constructs chromosome-scale pseudoassemblies from fragmented drafts using alignments to a reference assembly. GPatch produces complete, accurate, gap-free assemblies preserving over 95% of nucleotides from human and non-human draft genomes. We show that GPatch pseudoassemblies can be used to construct Hi-C matrices, whereas fragmented draft assemblies cannot. Until complete genome assembly becomes routine, GPatch presents a necessary tool for maximizing the utility of draft genomes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/655567v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@a8485aorg.highwire.dtl.DTLVardef@262cd9org.highwire.dtl.DTLVardef@4a67f8org.highwire.dtl.DTLVardef@efebc1_HPS_FORMAT_FIGEXP M_FIG C_FIG