hyphaltip

Jason Stajich's starred repositories

alphafold

Open source code for AlphaFold.

Language:PythonApache-2.012209 223 845

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

Language:HTMLCC-BY-SA-4.0932 89 8

dorado

Oxford Nanopore's Basecaller

Language:C++NOASSERTION464 32 964

manubot

Python utilities for Manubot: Manuscripts, open and automated

Language:PythonNOASSERTION423 16 149

cv

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greg

A command-line podcast aggregator

Language:PythonGPL-3.0295 13 94

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Language:JavaNOASSERTION249 23 640

bifrost

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Language:C++BSD-2-Clause200 12 72

nanofilt

Filtering and trimming of long read sequencing data

Language:PythonGPL-3.0183 10 58

bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Language:RGPL-3.0177 7 187

RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

Language:PythonMIT169 6 80

TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.

Language:C++GPL-3.0168 7 78

Comparative-Annotation-Toolkit

Language:PythonApache-2.0163 13 239

NECAT

Nanopore data assembler

Language:C132 9 55

datavzrd

A tool to create visual HTML reports from collections of CSV/TSV tables

Language:RustMIT87 2 74

cas-offinder

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

Language:C++NOASSERTION81 5 33

DeepTE

Neural network classification of TE

Language:PythonBSD-3-Clause78 7 33

Balrog

Bacterial Annotation by Learned Representation of Genes

Language:Jupyter NotebookMIT54 8 10

unite-train

🍄 Qiime2 ITS classifiers for the UNITE database

Language:HTMLBSD-3-Clause28 3 7

SprayNPray

Rapid and simple taxonomic profiling of genome and metagenome contigs

Language:PythonGPL-3.027 4 8

wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Language:PythonGPL-3.023 1 37

fastafs

toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files

Language:C++GPL-2.022 1 21

PyPHLAWD

Python version of PHLAWD

Language:PythonGPL-2.021 9 32

hercules

Profile HMM-based hybrid error correction algorithm for long reads

Language:C++BSD-3-Clause20 19 15

haplotypo

This is the Haplotypo repository

Language:PythonGPL-3.020 8 5

P_RNA_scaffolder

use paired-end transcriptome reads to scaffold genomes

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Phyla_AMPHORA

A Phylum-specific Automated Phylogenomic Inference Pipeline for Bacterial Sequences.

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ccgp_workflow

Snakemake+python workflow to highly parallelize variant calling in non-model organisms

Language:PythonMIT200

funbox

This is a singularity container designed to be a portable and complete funannotate black box.

Language:Shell2 30

kakapo_aspergillosis

Working directory for analysis of kākāpō _Aspergillus_ isolates

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