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DiscoSnp++ : de novo detection of small variants from raw unassembled read set(s)

https://doi.org/10.1101/209965

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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-642-16321-0_14openalex-snapshot

Identifying SNPs without a Reference Genome by Comparing Raw Reads

inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot

An integrated map of genetic variation from 1,092 human genomes

inferredcites →https://doi.org/10.1038/nbt.2515openalex-snapshot

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot

De novo assembly and genotyping of variants using colored de Bruijn graphs

inferredcites →https://doi.org/10.1038/ng.3121openalex-snapshot

Comprehensive variation discovery in single human genomes

inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot

A framework for variation discovery and genotyping using next-generation DNA sequencing data

inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot

Genotype and SNP calling from next-generation sequencing data

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/btr346openalex-snapshot

Paired-end RAD-seq forde novoassembly and marker design without available reference

inferredcites →https://doi.org/10.1093/bioinformatics/bts280openalex-snapshot

Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly

inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-snapshot

Informed and automated k -mer size selection for genome assembly

inferredcites →https://doi.org/10.1093/bioinformatics/btu406openalex-snapshot

GATB: Genome Assembly & Analysis Tool Box

inferredcites →https://doi.org/10.1093/bioinformatics/btv022openalex-snapshot

KMC 2: fast and resource-frugal k -mer counting

inferredcites →https://doi.org/10.1093/nar/gku1187openalex-snapshot

Reference-free detection of isolated SNPs

inferredcites →https://doi.org/10.1093/nar/gkw655openalex-snapshot

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

inferredcites →https://doi.org/10.1093/nar/gni035openalex-snapshot

Simple and highly efficient BAC recombineering using galK selection

inferredcites →https://doi.org/10.1101/gr.2395204openalex-snapshot

De Novo Repeat Classification and Fragment Assembly

inferredcites →https://doi.org/10.1145/974614.974643openalex-snapshot

De novo repeat classification and fragment assembly

inferredcites →https://doi.org/10.1186/1748-7188-8-22openalex-snapshot

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

inferredcites →https://doi.org/10.1371/journal.pgen.1003972openalex-snapshot

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

inferredcites →https://doi.org/10.1371/journal.pone.0060058openalex-snapshot

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

What points at this work

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

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Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

inferred← citeshttps://doi.org/10.1002/imt2.4openalex-snapshot

Applications of de Bruijn graphs in microbiome research

inferred← citeshttps://doi.org/10.1007/978-1-0716-2293-3_15openalex-snapshot

Alignment-Free Genotyping of Known Variations with MALVA

inferred← citeshttps://doi.org/10.1016/j.cels.2022.12.007openalex-snapshot

Pitfalls of genotyping microbial communities with rapidly growing genome collections

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Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola

inferred← citeshttps://doi.org/10.1016/j.isci.2019.07.011openalex-snapshot

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants

inferred← citeshttps://doi.org/10.1016/j.isci.2019.07.032openalex-snapshot

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

inferred← citeshttps://doi.org/10.1038/s41598-023-49462-xopenalex-snapshot

Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach)

inferred← citeshttps://doi.org/10.1093/aob/mcy113openalex-snapshot

Origin and parental genome characterization of the allotetraploidStylosanthes scabraVogel (Papilionoideae, Leguminosae), an important legume pasture crop

inferred← citeshttps://doi.org/10.1093/bioadv/vbab005openalex-snapshot

Comparative genome analysis using sample-specific string detection in accurate long reads

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab790openalex-snapshot

Theory of local k-mer selection with applications to long-read alignment

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PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting

inferred← citeshttps://doi.org/10.1093/molbev/msaf077openalex-snapshot

Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA)

inferred← citeshttps://doi.org/10.1093/nar/gkab025openalex-snapshot

Nebula: ultra-efficient mapping-free structural variant genotyper

inferred← citeshttps://doi.org/10.1093/nargab/lqab034openalex-snapshot

Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

inferred← citeshttps://doi.org/10.1101/2021.04.29.441957openalex-snapshot

How marine currents and environment shape plankton genomic differentiation: a mosaic view from Tara Oceans metagenomic data

inferred← citeshttps://doi.org/10.1101/2023.01.10.523380openalex-snapshot

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

inferred← citeshttps://doi.org/10.1101/2024.03.25.586631openalex-snapshot

Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA)

inferred← citeshttps://doi.org/10.1101/2025.07.08.663732openalex-snapshot

Identifying rare spontaneous mutations through wildtype E. coli population sequencing

inferred← citeshttps://doi.org/10.1101/599076openalex-snapshot

Linking Allele-Specific Expression And Natural Selection In Wild Populations

inferred← citeshttps://doi.org/10.1101/gr.279449.124openalex-snapshot

Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis

inferred← citeshttps://doi.org/10.1109/bibm49941.2020.9313433openalex-snapshot

Kmer2SNP: reference-free SNP calling from raw reads based on matching

inferred← citeshttps://doi.org/10.1111/1755-0998.12985openalex-snapshot

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea

inferred← citeshttps://doi.org/10.1128/jcm.01842-22openalex-snapshot

In Silico Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays

inferred← citeshttps://doi.org/10.1128/msphere.00482-19openalex-snapshot

Genomic Variation among Strains of Crithidia bombi and C. expoeki

inferred← citeshttps://doi.org/10.1186/s12859-020-03586-3openalex-snapshot

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

inferred← citeshttps://doi.org/10.1186/s12859-021-04018-6openalex-snapshot

Reliable genomic strategies for species classification of plant genetic resources

inferred← citeshttps://doi.org/10.1186/s12864-025-11722-7openalex-snapshot

A scalable distributed pipeline for reference-free variants calling

inferred← citeshttps://doi.org/10.1186/s12870-024-05628-xopenalex-snapshot

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

inferred← citeshttps://doi.org/10.1186/s13015-019-0137-8openalex-snapshot

SNPs detection by eBWT positional clustering

inferred← citeshttps://doi.org/10.1186/s13059-020-02244-4openalex-snapshot

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly

inferred← citeshttps://doi.org/10.3389/fgene.2021.615958openalex-snapshot

Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage

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Detecting Mutations by eBWT

inferred← citeshttps://doi.org/10.64898/2025.12.01.691650openalex-snapshot

bronko: ultrafast, alignment-free detection of viral genome variation

inferred← citeshttps://doi.org/10.70675/2ccfc627z786ez4b47zae5ez4477d6c63f74openalex-snapshot

Le plancton épipélagique marin du point de vue de la génomique des populations : une étude moléculaire à travers les données métagénomiques et métatranscriptomiques issues des expéditions de Tara Oceans

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Transcriptome and genome analysis based on alignment-free protocols

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DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

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