papers.md

• 2019 survey paper: A benchmark study of k-mer counting methods for high-throughput sequencing

• 2021 ht kmer: CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table

• 2017 survey: Next-generation sequencing: big datameets high performance computing

• Distributed-Memory k-mer Counting on GPUs

• NEST: DIMM based Near-Data-Processing Accelerator for K-mer Counting

• Optimizing High Performance Distributed Memory Parallel Hash Tables for DNA k-mer Counting

• Jellyfish

  • Homepage
  • V1 paper
  • V2 user guide

• Non-blocking hashtables with open addressing (Jellyfish hashtable)

• Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis -- Uses Kemerind for alignment on Xeon and Xeon Phi

• Multi-Core, Main-Memory Joins: Sort vs. Hash Revisited

-- Probalistic

• 2017 [Squeakr: An Exact and Approximate k-mer count System] (https://academic.oup.com/bioinformatics/article/34/4/568/4386917)
• 2023 April [KmerCo: KmerCo: A lightweight K-mer counting technique with a tiny memory footprint] ( https://arxiv.org/abs/2305.07545 )
• 2023 [KCOSS: an ultra-fast k-mer counter for assembled genome analysis] (https://academic.oup.com/bioinformatics/article/38/4/933/6443080)