Pinned Repositories
blactxm15-context-analysis
structural context analysis of genomic context around bla-ctx-m-15 gene
ecoliST131-structural-evo
snakemake pipeline for the analysis of structural genomic evolution of E. coli ST131
evo-genome-analysis
workflow for the genomic analysis of evolution experiments
genome-assembly
nextflow pipeline for parallel assembly of genomes using trycycler
kitp_qbio_bootcamp
Part of the tutorials for the kitp qbio school bioinformatics bootcamp
morbidostat-genome-analysis
analysis pipeline for morbidostat experiment data
nanopore-basecalling
Nextflow pipeline to perform live basecalling of nanopore reads on cpu/gpu on a cluster using SLURM.
pypangraph
Python package to manipulate pangenome graphs generated by PanGraph
sp_supplementary_reads
Student project repository. The short project consists in the analysis of secondary mappings from a morbidostat experiment.
pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
mmolari's Repositories
mmolari/pypangraph
Python package to manipulate pangenome graphs generated by PanGraph
mmolari/genome-assembly
nextflow pipeline for parallel assembly of genomes using trycycler
mmolari/affinity_maturation
This repository contains the code for the simulations and figures of the paper "Quantitative modeling of the effect of antigen dosage on the distribution of B-cell affinities in maturating germinal centers", by Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, and Rémi Monasson.
mmolari/blactxm15-context-analysis
structural context analysis of genomic context around bla-ctx-m-15 gene
mmolari/ecoliST131-structural-evo
snakemake pipeline for the analysis of structural genomic evolution of E. coli ST131
mmolari/evo-genome-analysis
workflow for the genomic analysis of evolution experiments
mmolari/kitp_qbio_bootcamp
Part of the tutorials for the kitp qbio school bioinformatics bootcamp
mmolari/morbidostat-genome-analysis
analysis pipeline for morbidostat experiment data
mmolari/nanopore-basecalling
Nextflow pipeline to perform live basecalling of nanopore reads on cpu/gpu on a cluster using SLURM.
mmolari/sp_supplementary_reads
Student project repository. The short project consists in the analysis of secondary mappings from a morbidostat experiment.
mmolari/phage_pangraph
pangraph analysis for phage diversity
mmolari/microbial_dset_download
pipeline to download all RefSeq records of a specific microbial species and sequence type
mmolari/nanopore_basecalling_kitp
snakemake pipeline to perform nanopore basecalling with dorado for kitp qbio course
mmolari/pairwise_chromosome_comparison
pipeline for the pairwise comparison of two similar chromosomes using pangraph
mmolari/rust_pangraph_benchmark
simple pipeline to benchmark the new rust implementation of pangraph
mmolari/structural-evo
Analysis of structural microbial genome evolution using pangraph
mmolari/wcs_tutorial
simple pangraph tutorial for WCS conference