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Research code accompanying AlphaGenome
AlphaFold 3 inference pipeline.
This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.
RawHash2 can accurately map raw nanopore signals to small and large reference genomes without basecalling in real-time. Described by Firtina et al. (published at https://academic.oup.com/bioinforma…
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Transformer-based sequence correction method for genome assembly polishing
A simplified version of Dorado built on top of S/BLOW5 format.
A small, auxiliary index to massively improve parallel fastq parsing
De novo assembler for single molecule sequencing reads using repeat graphs
Sequence correction provided by ONT Research
A comprehensive benchmarking framework for raw nanopore signal analysis, as described by Eris et al. (https://arxiv.org/pdf/2510.03629)
A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
[Nature Computational Science 2025] Real-time raw signal genomic analysis using fully integrated memristor hardware
A web app for ranking computer science departments according to their research output in selective venues, and for finding active faculty across a wide range of areas.
SegPore is a software to segment the raw signal of nanopore direct RNA sequencing and estimate the RNA modifications.
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
Deep learning framework for SV calling and genotyping
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
A tool for generating consensus long-read assemblies for bacterial genomes
A PyTorch Basecaller for Oxford Nanopore Reads
RUBICON is a novel framework to automatically develop deep-learning-based genomic basecallers for any given architecture, as described in our Genome Biology'24 paper https://genomebiology.biomedc
Rawasm is a patch to the popular miniasm tool. It enables the construction of genome assembly from raw nanopore signals.