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Detection and characterization of low and high genome coverage regions using an efficient running median and a double threshold approach

https://doi.org/10.1101/092478
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What this work says

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

inferredcites →https://doi.org/10.1016/0022-5193(77)90373-3openalex-snapshot
An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions
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/10.1016/j.cell.2016.06.017openalex-snapshot
A Landscape of Pharmacogenomic Interactions in Cancer
inferredcites →https://doi.org/10.1017/cbo9780511622762openalex-snapshot
Spectral Analysis for Physical Applications
inferredcites →https://doi.org/10.1038/jhg.2016.21openalex-snapshot
Evaluation of the evenness score in next-generation sequencing
inferredcites →https://doi.org/10.1038/nature724openalex-snapshot
The genome sequence of Schizosaccharomyces pombe
inferredcites →https://doi.org/10.1038/nbt0412-295openalex-snapshot
Oxford Nanopore announcement sets sequencing sector abuzz
inferredcites →https://doi.org/10.1038/nrg.2016.49openalex-snapshot
Coming of age: ten years of next-generation sequencing technologies
inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot
RNA-Seq: a revolutionary tool for transcriptomics
inferredcites →https://doi.org/10.1038/nrg2841openalex-snapshot
Advances in understanding cancer genomes through second-generation sequencing
inferredcites →https://doi.org/10.1038/nrg3642openalex-snapshot
Sequencing depth and coverage: key considerations in genomic analyses
inferredcites →https://doi.org/10.1073/pnas.69.10.2842openalex-snapshot
Bidirectional Replication of the Chromosome in Escherichia coli
inferredcites →https://doi.org/10.1088/0264-9381/19/7/338openalex-snapshot
Median based line tracker (MBLT): model independent and transient preserving line removal from interferometric data
inferredcites →https://doi.org/10.1088/0264-9381/22/23/004openalex-snapshot
GEO 600 online detector characterization system
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/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts480openalex-snapshot
Snakemake—a scalable bioinformatics workflow engine
inferredcites →https://doi.org/10.1093/bioinformatics/btt147openalex-snapshot
Analyzing genome coverage profiles with applications to quality control in metagenomics
inferredcites →https://doi.org/10.1093/bioinformatics/btt547openalex-snapshot
BioServices: a common Python package to access biological Web Services programmatically
inferredcites →https://doi.org/10.1093/bioinformatics/btv226openalex-snapshot
De novo meta-assembly of ultra-deep sequencing data
inferredcites →https://doi.org/10.1093/nar/gkn425openalex-snapshot
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
inferredcites →https://doi.org/10.1093/nar/gkq072openalex-snapshot
Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
inferredcites →https://doi.org/10.1101/006395openalex-snapshot
Error correction and assembly complexity of single molecule sequencing reads
inferredcites →https://doi.org/10.1101/gr.174730.114openalex-snapshot
Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1126/science.1162986openalex-snapshot
Real-Time DNA Sequencing from Single Polymerase Molecules
inferredcites →https://doi.org/10.1128/jvi.77.21.11546-11554.2003openalex-snapshot
A Molecularly Cloned Schwarz Strain of Measles Virus Vaccine Induces Strong Immune Responses in Macaques and Transgenic Mice
inferredcites →https://doi.org/10.1186/1471-2105-6-245openalex-snapshot
Extension of Lander-Waterman theory for sequencing filtered DNA libraries
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7490/f1000research.1112656.1openalex-snapshot
Sequana: a set of flexible genomic pipelines for processing and reporting NGS analysis

What points at this work

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

inferred← citeshttps://doi.org/10.1111/nph.71538openalex-snapshot
Selection shapes the evolution of genome size in a globally invasive plant
inferred← citeshttps://doi.org/10.1534/g3.120.401028openalex-snapshot
Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)
inferred← citeshttps://doi.org/10.21105/joss.00352openalex-snapshot
'Sequana': a Set of Snakemake NGS pipelines
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