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 …
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 …
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
… 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 …
profiled additional structural variations in the WS77111 genome in relation to PG29, including …
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
… 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 …
[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
… 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 …
… 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
… 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 …
… 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 …
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
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 …
available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields …
ntHash: recursive nucleotide hashing
… (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…
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 …
bp (or 30 amino acids), which occupied 1.4 Mb (24%) of genome sequence, including 1,065 …