Pierre Peterlongo
pierrepeterlongo
I’m designing models and algorithms for sequencing (NGS & TGS) data.
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Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
Comparing and combining multiple metagenomic datasets
Repositories
50Estimating k-mer coverage histogram of genomics data
ORI (Oxford nanopore Reads Identification) is a software allowing, from long nanopore reads, to identify the bacterial strains present in a sample.
How many distinct k-mers are there in a sequence?
A Rust tool for estimating number of distinct k-mers and number of *solid* kmers using Bloom filters.
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Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Logan-Search results) run a local blast between the query and the subset of contigs or unitigs containing at least one shared k-mer with the query.
back to sequences documentation
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Visualizing the number of solid canonical kmers while streaming reads
2025 hands-on tutorial on accessing Logan data and using logan-search
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Count kmers, sequences, nucleotides
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Count number of unique kmers from fasta or fasta.gz files
Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
Comparing and combining multiple metagenomic datasets
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A C++ API to read and write kff files
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A fast and compact k-mer index for large-scale matching and color queries.
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Intern candidate test
Fast genome and metagenome distance estimation using MinHash
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