BitMapper: an efficient all-mapper based on bit-vector computing.

A fast bit-vector algorithm for approximate string matching based on dynamic programming. Comparing variant call files for performance benchmarking of next-generation sequencing variant calling pipelines. Multi-platform discovery of haplotype-resolved structural variation in human genomes. An open resource for accurately benchmarking small variant and reference calls. A synthetic-diploid benchmark for accurate variant-calling evaluation. The design and construction of reference pangenome graphs with minigraph. Minimap2: pairwise alignment for nucleotide sequences. A diploid assembly-based benchmark for variants in the major histocompatibility complex. QUAST: quality assessment tool for genome assemblies. Flow cytometric determination of genome size in the Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Origin and evolution of the octoploid strawberry genome. Highly accurate long-read HiFi sequencing data for five complex genomes. Identifying and removing haplotypic duplication in primary genome assemblies. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Preprint at bioRxiv (2016).Įdge, P., Bafna, V. WhatsHap: fast and accurate read-based phasing. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Chromosome-scale, haplotype-resolved assembly of human genomes. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. De novo assembly of haplotype-resolved genomes with trio binning. Phased diploid genome assembly with single-molecule real-time sequencing. Efficient assembly of nanopore reads via highly accurate and intact error correction. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Fast and accurate long-read assembly with wtdbg2. Assembly of long, error-prone reads using repeat graphs. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. The hifiasm assemblies produced in this work are available at and. The CHM13 reference (v0.9) generated by the T2T consortium can be found at. For BUSCO, the Embryophyta, Tetrapoda and Mammalia datasets are available at, and, respectively. The HG002 major histocompatibility complex reference sequences can be found at (ref. The BAC libraries of CHM13 and HG00733 can be found at, respectively. These HG002 reads were downsampled to 30-fold coverage.

GIAB’s ‘homogeneity Run01’ short-read runs were used for the HG002 trio. For trio binning and computing QV, short reads were also downloaded: SRR7782677 for HG00733, ERR3241754 for HG00731 (father), ERR3241755 for HG00732 (mother) and SRX1082031 for CHM13. All HiFi data were obtained from the NCBI Sequence Read Archive: SRR11606869 for Z.

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