Repositories list

• mbi

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Nov 13, 2024Nov 13, 2024

• assembly-scripts

  Public
  A selection of scripts useful for genome assembly.

  Perl

  •

  MIT License

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• pridav_tutorials

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

• admm-pruning

  Public
  Python

  •

  MIT License

  •0•17•2•0•Updated Jul 22, 2024Jul 22, 2024

• mcdp2

  Public
  Tool for colocalization analysis for genomic annotations with genomic contexts

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 17, 2024Jun 17, 2024

• canParSR23

  Public
  Assembly of yeast Candida parapsilosis strain SR23

  Gnuplot

  •0•0•0•0•Updated May 18, 2024May 18, 2024

• neural-network-merging

  Public
  Jupyter Notebook

  •3•6•0•1•Updated Sep 20, 2023Sep 20, 2023

• warpstr

  Public
  Determining tandem repeat lengths using raw nanopore signals.

  Python

  •

  Other

  •1•12•4•0•Updated Sep 11, 2023Sep 11, 2023

• plasgraph2-datasets

  Public
  Datasets for training and testing plasgraph2

  0•0•0•0•Updated Aug 30, 2023Aug 30, 2023

• nadavca

  Public
  NAnopore DAta Variant CAller

  Python

  •

  Other

  •1•1•0•0•Updated Jun 27, 2023Jun 27, 2023

• virpool

  Public
  Tool for Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples

  Python

  •0•4•0•0•Updated Jun 19, 2023Jun 19, 2023

• pande-mic-dashboard

  Public
  Python

  •0•0•0•0•Updated May 25, 2023May 25, 2023

• pande-mic

  Public
  python & snake-make pipeline for live monitoring of nanopore sequenicng runs.

  bioinformaticssequencing

  Python

  •0•0•0•0•Updated May 25, 2023May 25, 2023

• y-mtptm

  Public
  JavaScript

  •

  GNU Lesser General Public License v3.0

  •0•0•0•0•Updated Apr 9, 2023Apr 9, 2023

• mcdp2-reproducibility

  Public
  Shell

  •0•0•0•0•Updated Jan 18, 2023Jan 18, 2023

• mc-overlaps

  Public
  Python

  •

  MIT License

  •0•3•0•0•Updated Oct 15, 2022Oct 15, 2022

• pfp_wg

  Public
  C

  •3•1•0•0•Updated Aug 12, 2022Aug 12, 2022

• deepnano-blitz

  Public
  Very fast ONT basecaller

  Rust

  •

  MIT License

  •12•52•4•1•Updated Jun 17, 2022Jun 17, 2022

• mc-overlaps-reproducibility

  Public
  0•0•0•0•Updated Jan 13, 2022Jan 13, 2022

• transducer_decoder

  Public
  Rust

  •

  Apache License 2.0

  •0•0•2•0•Updated Dec 1, 2021Dec 1, 2021

• osprey

  Public
  Fast bird catching fishes AKA realtime very high accuracy CPU basecaller for Oxford nanopore reads.

  C++

  •

  Apache License 2.0

  •1•15•0•0•Updated Oct 6, 2021Oct 6, 2021

• heron

  Public
  HAC nanopore basecaller

  Python

  •

  Apache License 2.0

  •2•6•1•0•Updated Oct 6, 2021Oct 6, 2021

• rampart

  Public
  Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

  JavaScript

  •

  GNU General Public License v3.0

  •34•0•0•2•Updated Sep 25, 2021Sep 25, 2021

• surveillance-itat-supplement

  Public
  0•0•0•0•Updated Aug 7, 2021Aug 7, 2021

• bcg-supplement

  Public
  Supplementary data for "Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression"

  0•0•0•0•Updated Aug 6, 2021Aug 6, 2021

• covid-pooling

  Public
  Code for a DARE workshop talk at ITAT 2021

  Python

  •0•0•0•0•Updated Jul 28, 2021Jul 28, 2021

• nanocrop

  Public
  Shell

  •0•0•1•2•Updated May 17, 2021May 17, 2021

• pheri

  Public
  Prediction of the phage hosts

  Python

  •

  MIT License

  •1•0•0•0•Updated May 10, 2021May 10, 2021

• Porechop

  Public
  adapter trimmer for Oxford Nanopore reads

  C++

  •

  GNU General Public License v3.0

  •128•0•0•0•Updated May 6, 2021May 6, 2021

• nanobeak

  Public
  0•0•0•1•Updated Apr 22, 2021Apr 22, 2021