Logan Unitigs and Contigs

PBSIM3: a simulator for all types of PacBio and ONT long reads

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Classifier for metagenomic sequences

MetageNN is a proof of concept neural network used to obtain a memory-efficient taxonomic classifier robust to sequencing errors and missing genomes

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

MetScale: snakemake workflows to scale metagenome analyses

🧬 gget enables efficient querying of genomic reference databases

A fast and sensitive gapped read aligner

A package for designing compact and comprehensive capture probe sets.

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…

Official git repository for Biopython (originally converted from CVS)

BSSE COVID-19 sequencing of test swab samples

Depth-weighted De-Mixing

CAMISIM: Simulating metagenomes and microbial communities

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

A SARS-CoV-2 Mutation Pattern Query Tool

Med-BERT, contextualized embedding model for structured EHR data

EMNLP'22 | MedCLIP: Contrastive Learning from Unpaired Medical Images and Texts

Code for "Graph Neural Network on Electronic Health Records for Predicting Alzheimer’s Disease"

Deep Learning with Multimodal Representation for Pancancer Prognosis Prediction

Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium. These files can be used as standard resource of BED files …