Benjamin P. Vandervalk
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Tigmint: correcting assembly errors using linked reads from large molecules Open
Scaffolding an assembly that has been corrected with Tigmint yields a final assembly that is both more correct and substantially more contiguous than an assembly that has not been corrected. Using single-molecule sequencing in combination …
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers Open
ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implemen…
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers Open
Background The long-range sequencing information captured by linked reads, such as those available from 10x Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce AR…
Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules Open
Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in th…
Tigmint: correct assembly errors using linked reads from large molecules Open
Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in th…
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data Open
Motivation Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely relate…
View article: ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter Open
The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps toward elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species,…
View article: Kollector: transcript-informed, targeted <i>de novo</i> assembly of gene loci
Kollector: transcript-informed, targeted <i>de novo</i> assembly of gene loci Open
Motivation Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise.…
View article: It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)
It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana) Open
Frogs play important ecological roles as sentinels, insect control and food sources. Several species are important model organisms for scientific research to study embryogenesis, development, immune function, and endocrine signaling. The g…
Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data Open
The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of D…
View article: ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter
ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter Open
The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps towards elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species…
ntHash: recursive nucleotide hashing Open
Motivation Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, k-mer counting and error correction. Hence, ex…
Organellar genomes of white spruce (<i>Picea glauca</i>): assembly and annotation Open
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, an…