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PaKman : Scalable Assembly of Large Genomes on Distributed Memory Machines

https://doi.org/10.1101/523068
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-319-05269-4_4openalex-snapshot
On the Representation of de Bruijn Graphs
inferredcites →https://doi.org/10.1007/978-3-642-27848-8_573-1openalex-snapshot
Min-Hash Sketches
inferredcites →https://doi.org/10.1016/j.jpdc.2007.05.014openalex-snapshot
Assembling genomes on large-scale parallel computers
inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1073/pnas.171285098openalex-snapshot
An Eulerian path approach to DNA fragment assembly
inferredcites →https://doi.org/10.1089/cmb.2009.0238openalex-snapshot
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/bti1114openalex-snapshot
The fragment assembly string graph
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.097261.109openalex-snapshot
De novo assembly of human genomes with massively parallel short read sequencing
inferredcites →https://doi.org/10.1101/gr.214346.116openalex-snapshot
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
inferredcites →https://doi.org/10.1109/icpp.2016.29openalex-snapshot
SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Extreme Scale
inferredcites →https://doi.org/10.1109/ipdps.2006.1639259openalex-snapshot
Assembling genomes on large-scale parallel computers
inferredcites →https://doi.org/10.1109/ipdps.2010.5470397openalex-snapshot
Parallel de novo assembly of large genomes from high-throughput short reads
inferredcites →https://doi.org/10.1109/sc.2014.41openalex-snapshot
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly
inferredcites →https://doi.org/10.1109/tcbb.2017.2737999openalex-snapshot
FastEtch: A Fast Sketch-Based Assembler for Genomes
inferredcites →https://doi.org/10.1145/2807591.2807664openalex-snapshot
HipMer
inferredcites →https://doi.org/10.1145/2975167.2975192openalex-snapshot
A Fast Sketch-based Assembler for Genomes
inferredcites →https://doi.org/10.1186/1471-2105-12-354openalex-snapshot
Parallelized short read assembly of large genomes using de Bruijn graphs
inferredcites →https://doi.org/10.1186/1471-2105-15-s2-s2openalex-snapshot
On the selection of appropriate distances for gene expression data clustering
inferredcites →https://doi.org/10.1186/1471-2105-15-s9-s2openalex-snapshot
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
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