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LanzaTech

Chicago, IL

linkedin.com/in/drbrowne/

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Dan Browne's starred repositories

altair

Declarative statistical visualization library for Python

Language:PythonBSD-3-Clause8995 141 1948

Prodigal

Prodigal Gene Prediction Software

Language:CGPL-3.0412 26 97

GeneGPT

Code and data for GeneGPT.

Language:PythonNOASSERTION358 18 4

Roary

Rapid large-scale prokaryote pan genome analysis

Language:PerlNOASSERTION299 29 393

CAT_pack

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

Language:PythonMIT164 9 93

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

Language:PythonGPL-3.0128 4 149

infernal

RNA secondary structure/sequence profiles for homology search and alignment

Language:CNOASSERTION99 13 37

RiboDetector

Accurate and rapid RiboRNA sequences Detector based on deep learning

Language:PythonGPL-3.089 5 50

metaMDBG

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

Language:C++MIT77 4 9

minipileup

Simple pileup-based variant caller

Language:C77 4 11

GenoVi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

Language:PythonNOASSERTION66 4 19

PHANOTATE

PHANOTATE: a tool to annotate phage genomes.

Language:PythonGPL-3.065 10 24

PhiSpy

Prediction of prophages from bacterial genomes

Language:Jupyter NotebookMIT64 10 52

phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

Language:PythonMIT64 2 37

ntSynt

Detecting multi-genome synteny using minimizer graph mapping

Language:PythonGPL-3.061 5 1

ska.rust

Split k-mer analysis – version 2

Language:RustApache-2.056 4 34

tRNAscan-SE

A program for detection of tRNA genes

Language:CGPL-3.052 8 37

charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

Language:PythonNOASSERTION49 19 163

STRONG

Strain Resolution ON Graphs

Language:PythonMIT44 8 116

CBL

A Rust library providing fully dynamic sets of k-mers with high locality

Language:RustMIT42 2 3

MetaCoAG

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Language:PythonGPL-3.042 1 35

piggy

Pipeline for analysing intergenic regions in bacteria

Language:PerlGPL-3.036 5 28

LiftOn

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

Language:PythonGPL-3.036 1 5

centrifuger

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

Language:C++MIT32 3 4

polygraph

Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.

Language:Jupyter NotebookMIT24 7 3

DeepProZyme

DeepECtransformer

Language:Jupyter Notebook17 2 6

ribovore

Language:PerlNOASSERTION13 5 4

ProkFunFind

🦠 A tool for identifying and analyzing functions in microbial genomes.

Language:PythonNOASSERTION11 2 2

Sequeduct

Sequencing analysis pipeline

Language:NextflowGPL-3.010 6 1

MetagenomicKG

Language:Python10 2 1