Pierre Peterlongo's repositories
kmer2sequences
Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
quasi_dictionary
Data structure indexing key-values with controled false positive rate and with low time and memory impacts
b2s_doc
back to sequences documentation
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.
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.
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
Mash
Fast genome and metagenome distance estimation using MinHash
negative_binomial
Code for fitting a negative binomial distribution in Python
ntCard
Estimating k-mer coverage histogram of genomics data
py-upset
A pure-python implementation of the UpSet suite of visualisation methods by Lex, Gehlenborg et al.
strainberry
Automated strain separation of low-complexity metagenomes
UpSetPlot
Draw UpSet plots with Matplotlib
vg
tools for working with genome variation graphs