Projects | Open Source Science

Projects

Scientific Software

Updated 10 months ago

sourmash v4 — Peer-reviewed • Rank 21.8 • Science 100%

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets - Published in JOSS (2024)

bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling

Scientific Software · Peer-reviewed

Scientific Software

Updated 10 months ago

TipToft — Peer-reviewed • Rank 8.3 • Science 100%

TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)

bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases kmer long-reads nanopore oxford-nanopore pacbio pathogen plasmid plasmidfinder research uncorrected

Biology

Scientific Software · Peer-reviewed

Updated 10 months ago

kmermaid • Rank 5.7 • Science 57%

k-mer similarity analysis pipeline

k-mer kmer kmer-counting kmer-frequency-count nextflow nf-core pipeline workflow

Updated 10 months ago

seqR • Rank 4.8 • Science 10%

fast and comprehensive k-mer counting package

bioinformatics bioinformatics-tool dna-processing feature-engineering feature-extraction genomics hashing hashing-algorithms k-mer k-mer-counting kmer kmer-counting kmer-frequency-count kmers ngram ngrams protein-sequences rcpp rcppparallel rpackage

Updated 10 months ago

https://github.com/alexpreynolds/kmer-collapse • Rank 1.1 • Science 13%

Collapse a set of redundant kmers to use IUPAC degenerate bases

bioinformatics encoding iupac kmer

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-abseil • Rank 0.0 • Science 13%

Count canonical kmers with Abseil C++ `absl::flat_hash_map`

abseil bazel bazel-examples bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-unordmap • Science 13%

Count canonical kmers with STL unordered_map

bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/alexpreynolds/kmer-boolean • Science 13%

Test if a kmer is or is not in a set of sequences

bioinformatics cpp14 kmer kmer-composition python

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-emilib • Science 13%

Count canonical kmers with Emil Ernerfeldt's emilib::HashMap

bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-ska • Science 13%

Count canonical kmers with Malte Skarupke's bytell_hash_map hash table

bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-boost • Science 13%

Count canonical kmers with Boost C++ `boost::unordered_map` hash table

bazel bazel-examples bioinformatics boost cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/alexpreynolds/kmer-counter-sparse • Science 13%

Count canonical kmers with Google sparse_hash_map

bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Updated 10 months ago

https://github.com/brentp/nim-kmer • Science 13%

DNA kmer operations for nim

genomics kmer nim-lang

Updated 10 months ago

kmer-counter • Science 44%

Count kmers with a more efficient (faster) hash table

bioinformatics cpp14 genomics hash-map kmer kmer-counting