16 citations · 41 across the 6 of their papers we have counts for
10 papers
Metagenome assembly of high-fidelity long reads with hifiasm-meta
Xiaowen Feng, Haoyu Cheng, Daniel Portik +1
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome asse…
Robust haplotype-resolved assembly of diploid individuals without parental data
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo +4
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction dat…
New strategies to improve minimap2 alignment accuracy
Heng Li
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly…
Twelve years of SAMtools and BCFtools
Petr Danecek, James K. Bonfield, Jennifer Liddle +8
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago…
Haplotype-resolved de novo assembly with phased assembly graphs
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng +2
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into…
The design and construction of reference pangenome graphs
Heng Li, Xiaowen Feng, Chong Chu
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to m…