ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

SD Jackman, BP Vandervalk, H Mohamadi… - Genome …, 2017 - genome.cshlp.org
… (paired-end 250 bp) data and the availability of … bp sequencing data from an Illumina HiSeq
2500 in rapid-run mode is currently roughly double the cost per base of paired-end 125-bp

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

…, MMS Yuen, CI Keeling, D Brand, BP Vandervalk… - …, 2013 - academic.oup.com
bp kit on the HiSeq 2000, we generated PET reads from two libraries with 250 bp nominal
fragment lengths and 18 libraries with 500 bp … 300 bp PET reads from four libraries with 500 bp

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

…, A Raymond, GA Taylor, BP Vandervalk… - The Plant …, 2015 - Wiley Online Library
… When considering WS77111 scaffolds 500 bp or larger for alignments ≥100 bp, we
profiled additional structural variations in the WS77111 genome in relation to PG29, including …

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

RL Warren, C Yang, BP Vandervalk, B Behsaz… - …, 2015 - academic.oup.com
bp, indicative of overlaps 400 bp or greater between contigs). Running SSPACE-LongRead
[25] (Table 1E) gave comparable results to that of LINKS (Table 1D), producing a marginally …

[HTML][HTML] Sealer: a scalable gap-closing application for finishing draft genomes

D Paulino, RL Warren, BP Vandervalk, A Raymond… - BMC …, 2015 - Springer
… When running individual Sealer runs at unique values of k on 250 bp human experimental
… Generally speaking, k-mers varying in size from 60 to 220 bp were all suited to close gaps …

[HTML][HTML] Tigmint: correcting assembly errors using linked reads from large molecules

…, L Coombe, J Chu, RL Warren, BP Vandervalk… - BMC …, 2018 - Springer
… Tigmint checks that each region of a fixed size specified by the user, 1000 bp by default, is
… a sliding window of 1000 bp (by default) with a step size of 1 bp. Tigmint cuts the assembly …

[HTML][HTML] The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

SA Hammond, RL Warren, BP Vandervalk… - Nature …, 2017 - nature.com
… , which ranged in length from 200 bp to almost 11 kb, with a median length of 973 bp. … the
absence of a 161 bp sequence at coordinate 15,270, and a 12-bp insertion at coordinate 9214 …

[HTML][HTML] ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

L Coombe, J Zhang, BP Vandervalk, J Chu… - BMC …, 2018 - Springer
Background The long-range sequencing information captured by linked reads, such as those
available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields …

ntHash: recursive nucleotide hashing

H Mohamadi, J Chu, BP Vandervalk, I Birol - Bioinformatics, 2016 - academic.oup.com
… (b) Runtime for hashing 250 bp DNA sequences with different k-mer lengths from 50 to
250. ntHash outperforms all other hash methods when hashing more than two subsequent k-mers…

Organellar Genomes of White Spruce ( Picea glauca ): Assembly and Annotation

…, RL Warren, EA Gibb, BP Vandervalk… - Genome Biology and …, 2016 - academic.oup.com
… In addition to 106 protein-coding genes, we found an additional 6,265 ORFs of least 90
bp (or 30 amino acids), which occupied 1.4 Mb (24%) of genome sequence, including 1,065 …