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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

https://doi.org/10.1101/698910
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What this work says

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

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Genomic mapping by fingerprinting random clones: A mathematical analysis
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Biological sequence analysis
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Erythrocyte Binding Protein PfRH5 Polymorphisms Determine Species-Specific Pathways of Plasmodium falciparum Invasion
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Characterization of pairwise and multiple sequence alignment errors
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PacBio Sequencing and its Applications
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Frequent recombination events generate diversity within the multi-copy variant antigen gene families of Plasmodium falciparum
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Ectopic Recombination of a Malaria var Gene during Mitosis Associated with an Altered var Switch Rate
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Intra-cluster recombination and var transcription switches in the antigenic variation of Plasmodium falciparum
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Biological Sequence Analysis
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Chloroquine resistance not linked to mdr-like genes in a Plasmodium falciparum cross
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Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum
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Genome sequence of the human malaria parasite Plasmodium falciparum
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Hybrid error correction and de novo assembly of single-molecule sequencing reads
inferredcites →https://doi.org/10.1038/nbt.4060openalex-snapshot
Nanopore sequencing and assembly of a human genome with ultra-long reads
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De novo assembly and genotyping of variants using colored de Bruijn graphs
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A genome-wide map of diversity in Plasmodium falciparum
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Sense from sequence reads: methods for alignment and assembly
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Mechanisms underlying structural variant formation in genomic disorders
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Genome structural variation discovery and genotyping
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Artemisinin resistance phenotypes and K13 inheritance in a Plasmodium falciparum cross and Aotus model
inferredcites →https://doi.org/10.1073/pnas.88.8.3382openalex-snapshot
Genetic mapping of the chloroquine-resistance locus on Plasmodium falciparum chromosome 7.
inferredcites →https://doi.org/10.1093/bioinformatics/btq697openalex-snapshot
Succinct data structures for assembling large genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btu538openalex-snapshot
LoRDEC: accurate and efficient long read error correction
inferredcites →https://doi.org/10.1093/bioinformatics/btx067openalex-snapshot
Succinct colored de Bruijn graphs
inferredcites →https://doi.org/10.1093/bioinformatics/btx471openalex-snapshot
Faucet: streaming de novo assembly graph construction
inferredcites →https://doi.org/10.1093/bioinformatics/bty157openalex-snapshot
Integrating long-range connectivity information into de Bruijn graphs
inferredcites →https://doi.org/10.1093/carcin/bgu099openalex-snapshot
An expanding universe of the non-coding genome in cancer biology
inferredcites →https://doi.org/10.1093/genetics/165.4.2213openalex-snapshot
Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/gigascience/gix038openalex-snapshot
Alignment of 1000 Genomes Project reads to reference assembly GRCh38
inferredcites →https://doi.org/10.1093/molbev/msy059openalex-snapshot
De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
inferredcites →https://doi.org/10.1093/nar/gkt1174openalex-snapshot
DNA secondary structures are associated with recombination in majorPlasmodium falciparumvariable surface antigen gene families
inferredcites →https://doi.org/10.1093/nar/gkw292openalex-snapshot
Companion : a web server for annotation and analysis of parasite genomes
inferredcites →https://doi.org/10.1101/024182openalex-snapshot
Genome variation and meiotic recombination in Plasmodium falciparum : insights from deep sequencing of genetic crosses
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.191395.115openalex-snapshot
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
inferredcites →https://doi.org/10.1101/gr.203711.115openalex-snapshot
Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
inferredcites →https://doi.org/10.1126/science.3299700openalex-snapshot
Genetic Analysis of the Human Malaria Parasite Plasmodium falciparum
inferredcites →https://doi.org/10.1186/1471-2148-13-110openalex-snapshot
Hypervariable antigen genes in malaria have ancient roots
inferredcites →https://doi.org/10.1186/1471-2164-15-737openalex-snapshot
Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt
inferredcites →https://doi.org/10.1186/cc2183openalex-snapshot
Clinical review: Severe malaria.
inferredcites →https://doi.org/10.1186/gb-2004-5-10-242openalex-snapshot
Hotspots of homologous recombination in the human genome: not all homologous sequences are equal.
inferredcites →https://doi.org/10.1186/gm42openalex-snapshot
Genomic disorders ten years on
inferredcites →https://doi.org/10.1186/s13059-015-0633-1openalex-snapshot
Detecting non-allelic homologous recombination from high-throughput sequencing data
inferredcites →https://doi.org/10.1201/9781420035346openalex-snapshot
CRC Standard Mathematical Tables and Formulae
inferredcites →https://doi.org/10.1201/b10980openalex-snapshot
CRC Standard Mathematical Tables and Formulae
inferredcites →https://doi.org/10.1371/journal.pgen.1003293openalex-snapshot
Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families
inferredcites →https://doi.org/10.1371/journal.pgen.1004812openalex-snapshot
Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.3389/fbioe.2015.00092openalex-snapshot
Detection of Genomic Structural Variants from Next-Generation Sequencing Data
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2020.06.22.164186openalex-snapshot
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
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