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Correcting bias from stochastic insert size in read pair data — applications to structural variation detection and genome assembly

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-642-02008-7_16openalex-snapshot

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

inferredcites →https://doi.org/10.1007/978-3-642-20036-6_40openalex-snapshot

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

inferredcites →https://doi.org/10.1016/0888-7543(88)90007-9openalex-snapshot

Genomic mapping by fingerprinting random clones: A mathematical analysis

inferredcites →https://doi.org/10.1038/nature07517openalex-snapshot

Accurate whole human genome sequencing using reversible terminator chemistry

inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot

The Norway spruce genome sequence and conifer genome evolution

inferredcites →https://doi.org/10.1038/nmeth.1363openalex-snapshot

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

inferredcites →https://doi.org/10.1089/cmb.2011.0170openalex-snapshot

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btq683openalex-snapshot

Scaffolding pre-assembled contigs using SSPACE

inferredcites →https://doi.org/10.1093/bioinformatics/btr562openalex-snapshot

Fast scaffolding with small independent mixed integer programs

inferredcites →https://doi.org/10.1093/bioinformatics/bts175openalex-snapshot

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/bts441openalex-snapshot

Improved gap size estimation for scaffolding algorithms

inferredcites →https://doi.org/10.1093/bioinformatics/bts566openalex-snapshot

CLEVER: clique-enumerating variant finder

inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot

Mapping short DNA sequencing reads and calling variants using mapping quality scores

inferredcites →https://doi.org/10.1101/gr.131383.111openalex-snapshot

GAGE: A critical evaluation of genome assemblies and assembly algorithms

inferredcites →https://doi.org/10.1101/gr.138925.112openalex-snapshot

Paired-end sequencing of Fosmid libraries by Illumina

inferredcites →https://doi.org/10.1101/gr.141515.112openalex-snapshot

Finished bacterial genomes from shotgun sequence data

inferredcites →https://doi.org/10.1186/1471-2105-11-345openalex-snapshot

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

inferredcites →https://doi.org/10.1186/1471-2105-15-281openalex-snapshot

BESST - Efficient scaffolding of large fragmented assemblies

inferredcites →https://doi.org/10.1186/1756-0500-6-334openalex-snapshot

De novo likelihood-based measures for comparing genome assemblies

inferredcites →https://doi.org/10.1186/gb-2013-14-5-r47openalex-snapshot

REAPR: a universal tool for genome assembly evaluation

inferredcites →https://doi.org/10.1371/journal.pone.0003373openalex-snapshot

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

inferredcites →https://doi.org/10.1371/journal.pone.0008407openalex-snapshot

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

inferredcites →https://doi.org/10.1371/journal.pone.0031002openalex-snapshot

Feature-by-Feature – Evaluating De Novo Sequence Assembly

inferredcites →https://doi.org/10.1534/genetics.113.159715openalex-snapshot

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1186/s13059-020-01993-6openalex-snapshot

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1200983openalex-snapshot

bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting

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