angiehinrichs Goto Github PK

augur

Pipeline components for real-time phylodynamic analysis

bioconda-recipes

Conda recipes for the bioconda channel.

constellations

covid-19-lab-specific-bias-filter

We developed a tool to systematically flag COVID-19 genomes for variants resulting from possible lab specific biases. The program requires a concurrent nextstrain VCF file, nextstrain parsimony file and nextstrain metadata file as input. It outputs two tsv files: one with each flagged snp and the respective reasoning underlying the flag, and another providing more detailed information on each flagged lab.

g-nest

The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository G-NEST_examples:

hgvslib

hgvslib provides functions to parse and compare the equivalency of variant strings described according to Human Genome Variation Society (HGVS) syntax.

lineages-website

mpxv-lineage-designation

Updates and details of monkeypox virus lineages designations

ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

nhoodstats

science project: find gene clusters for various window sizes, compute avg neighborhood correlation & p-values

pango-designation

Repository for suggesting new lineages that should be added to the current scheme

pangolearn

Store of the trained model for pangolin to access.

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

pangolin-assignment

The latest lineage assignments from pangolin.

pangolin-data

Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments

samtabix

This is a merge of AngieHinrichs/samtools (lh3/samtools patched to allow alternate network lib and not check EOF) and tabix-0.2.6 downloaded from samtools.sourceforge.net. I replaced samtools' bgzf.[ch] with tabix's because tabix's seemed more recent. Had to modify some samtools files to work with updated bgzf.h.

samtools

This is Angie Hinrichs' fork of Heng Li's lh3/samtools, which describes itself as "*NOT* the official repository of samtools"; therefore this is even less official. I have applied a patch that adds a wrapper mode to knetfile, so that alternate network libraries (such as UCSC Genome Browser's kent/src/) can be hooked in.

sars-cov-2_sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

sarscov2lineages

sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences

strain_phylogenetics

usher

Ultrafast Sample Placement on Existing Trees

usher_demo

usher_wiki

docs holder for usher wiki