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alg_2020

back_to_sequences

benchmphf

Benchmark of two minimal perfect hash libraries (phf, emphf)

bloomtest

Intern candidate test

braw

Box of not RelAted Work

c-plus-plus-serializer

A minimal C++11 header only serializer. Can serialize basic types, strings, containers, maps and custom classes. No suppprt yet for pointer types.

carnac-lr

commet

Comparing and combining multiple metagenomic datasets

discosnp

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

div_labri_fall2019

fulgor

A fast and compact k-mer index for large-scale matching and color queries.

gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

haplosim

Simulate haplotypes according to a random markovian chain along a binary evolutionnary tree and generate metagenomic illumina data from a random admixture of simulated haplotypes

kff-reference

Contains the description of a file format to store kmers and associated values

kmer2sequences

Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.

kmindex_benchmarks

kmtricks_benchmarks

mash

Fast genome and metagenome distance estimation using MinHash

methmap

negative_binomial

Code for fitting a negative binomial distribution in Python

ntcard

Estimating k-mer coverage histogram of genomics data

pac

py-upset

A pure-python implementation of the UpSet suite of visualisation methods by Lex, Gehlenborg et al.

quasi_dictionary

Data structure indexing key-values with controled false positive rate and with low time and memory impacts

short_read_connector

sse2

Unusual uses of SSE2 registers

strainberry

Automated strain separation of low-complexity metagenomes

strainflair

tara_kmer_profiles

upsetplot

Draw UpSet plots with Matplotlib