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List of genomics software utilising sketching algorithms

ABySS genome assembly Bloom filter
BBsketch sequence analysis MinHash
BIGSI sequence index and search Bloom filter
FastEtch genome assembly Count-Min Sketch
ganon metagenome classification Bloom filter
GROOT variant detection in metagenomes MinHash (KHF)
HowDE Sequence Bloom Trees sequence index and search Bloom filter
HULK sequence analysis Histosketch
KmerGenie sequence analysis ntCard
Lighter sequence error correction Bloom filter
MC-MinH sequence clustering MinHash (KHF)
PopPUNK sequence clustering MinHash (KMV)
MHAP genome assembly MinHash (KMV)
Mantis sequence index and search Counting Quotient Filter
MashMap long read alignment MinHash (KMV)
MiniMap2 read alignment Minimizer
SeqOthello sequence index and search Minimum Perfect Hashing (Othello)
Sequence Bloom Trees sequence index and search Bloom filter
Split Sequence Bloom Trees sequence index and search Bloom filter
Squeakr sequence analysis Counting Quotient Filter
dashing sequence analysis HyperLogLog
finch sequence analysis MinHash (KMV)
khmer nucleotide sequence analysis Count-Min sketch
krakenUniq metagenome classification HyperLogLog
kssd sequence analysis K-mer Substring Space Decomposition
mash sequence analysis MinHash (KMV)
mashtree phylogenetic tree construction MinHash (KMV)
ntCard sequence analysis ntCard
sourmash sequence analysis MinHash (KMV)

last updated: 23.09.2019

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