Angie Hinrichs's repositories
nhoodStats
science project: find gene clusters for various window sizes, compute avg neighborhood correlation & p-values
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.
augur
Pipeline components for real-time phylodynamic analysis
avian-influenza
Consensus sequences for U.S. H5N1 clade 2.3.4.4b
bioconda-recipes
Conda recipes for the bioconda channel.
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:
lineage-designation-A
RSV-A lineage definitions and proposals
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.
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
SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
sarscov2phylo
Global phylogenies of SARS-CoV-2 sequences
usher
Ultrafast Sample Placement on Existing Trees
usher_wiki
docs holder for usher wiki