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Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs

https://doi.org/10.1101/236711
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What this work says

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

inferredcites →https://doi.org/10.1007/978-1-4419-7089-3_15openalex-snapshot
MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract
inferredcites →https://doi.org/10.1007/978-3-319-07959-2_28openalex-snapshot
From Theory to Practice: Plug and Play with Succinct Data Structures
inferredcites →https://doi.org/10.1007/978-3-319-56970-3_16openalex-snapshot
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees
inferredcites →https://doi.org/10.1007/978-3-642-33122-0_18openalex-snapshot
Succinct de Bruijn Graphs
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nature06244openalex-snapshot
The Human Microbiome Project
inferredcites →https://doi.org/10.1038/nature14962openalex-snapshot
The UK10K project identifies rare variants in health and disease
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nbt.3442openalex-snapshot
Fast search of thousands of short-read sequencing experiments
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/10.1073/pnas.171285098openalex-snapshot
An Eulerian path approach to DNA fragment assembly
inferredcites →https://doi.org/10.1089/cmb.2010.0252openalex-snapshot
Cactus Graphs for Genome Comparisons
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/btu014openalex-snapshot
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btx067openalex-snapshot
Succinct colored de Bruijn graphs
inferredcites →https://doi.org/10.1093/bioinformatics/btx261openalex-snapshot
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph
inferredcites →https://doi.org/10.1093/nar/gkv1276openalex-snapshot
GenBank
inferredcites →https://doi.org/10.1101/138016openalex-snapshot
Rainbowfish: A Succinct Colored de Bruijn Graph Representation
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.214155.116openalex-snapshot
Genome graphs and the evolution of genome inference
inferredcites →https://doi.org/10.1126/science.1251385openalex-snapshot
Comparative genomics reveals insights into avian genome evolution and adaptation
inferredcites →https://doi.org/10.1145/1290672.1290680openalex-snapshot
Succinct indexable dictionaries with applications to encoding k -ary trees, prefix sums and multisets
inferredcites →https://doi.org/10.1145/2213556.2213586openalex-snapshot
The wavelet trie
inferredcites →https://doi.org/10.1145/321812.321820openalex-snapshot
Efficient Storage and Retrieval by Content and Address of Static Files
inferredcites →https://doi.org/10.1145/42411.42420openalex-snapshot
The world's fastest Scrabble program
inferredcites →https://doi.org/10.1186/1751-0473-9-13openalex-snapshot
biobambam: tools for read pair collation based algorithms on BAM files
inferredcites →https://doi.org/10.1186/s13015-016-0066-8openalex-snapshot
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
inferredcites →https://doi.org/10.1186/s13015-017-0109-9openalex-snapshot
A graph extension of the positional Burrows–Wheeler transform and its applications
inferredcites →https://doi.org/10.1186/s13059-016-0917-0openalex-snapshot
The real cost of sequencing: scaling computation to keep pace with data generation
inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot
Mash: fast genome and metagenome distance estimation using MinHash
inferredcites →https://doi.org/10.1371/journal.pone.0101271openalex-snapshot
These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-030-32686-9_22openalex-snapshot
An Index for Sequencing Reads Based on the Colored de Bruijn Graph
inferred← citeshttps://doi.org/10.1016/j.isci.2019.06.035openalex-snapshot
Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going?
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa546openalex-snapshot
Succinct dynamic de Bruijn graphs
inferred← citeshttps://doi.org/10.1186/s13015-022-00212-0openalex-snapshot
Space-efficient representation of genomic k-mer count tables
inferred← citeshttps://doi.org/10.3929/ethz-b-000236144openalex-snapshot
Efficient graph-color compression with neighborhood-informed Bloom filters
inferred← citeshttps://doi.org/10.70675/3fec2ac9z833az4af2zaaa0zb650bd49bc2aopenalex-snapshot
Sketching data structures for alignment-free analysis of genomic sequences
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