ld-tools: toolkit for linkage disequilibrium calculation designed to work locally
Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog
Annotation pipeline for HPDS
Сompute support for ALT and REF alleles from aligned reads
Detect short tandem repeats (STRs) and call repeat expansions from long-read (Oxford Nanopore) BAM files — motif discovery, per-allele repeat length, coverage, and visual reports.
SOLARA - open-source solar + battery storage optimization platform built on NREL PySAM. Techno-economic analysis, NSGA-II / Bayesian / ML-surrogate optimization, NEC 2023 compliance checks and an interactive Dash dashboard.
Progetto di Elementi di Bioinformatica, A.A. 2021/2022
Tools to discover natural selection given multiple evolved DNA sequences (e.g., gnomad cohort, or multiple tumor samples)
Interactive desktop app for viewing sequencing coverage from BAM alignments
142 MW PV + 50 MW CSP trough hybrid plant with thermal storage in Spain, PySAM modelling, MILP dispatch optimisation, genetic algorithm sizing
Investigating unmapped reads within next generation sequencing data will provide additional information regarding the source of the trace microbial reads.
Bioinformatics CLI tool to generate WIG tracks from SAM/BAM files
Stratified variant-calling evaluation on GIAB chr20. Aggregate F1 hides 35x of the effect; skipping confident-region restriction penalises the better caller 4.5x.
Pysam module (python2.7) singularity container
Python toolkit for converting BAM/SAM alignments into coverage, SNP, and indel overviews, with SCG-based normalization and R/ggplot2 visualization
vue app with flask REST api to process genomic data
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