angiehinrichs Goto Github PK
Name: Angie Hinrichs
Type: User
Company: @ucscGenomeBrowser
Bio: UCSC Genome Browser developer since 2002; UShER/SARS-CoV-2 since 2020
Twitter: AngieSHinrichs
Location: California
Blog: http://genome.ucsc.edu/
Name: Angie Hinrichs
Type: User
Company: @ucscGenomeBrowser
Bio: UCSC Genome Browser developer since 2002; UShER/SARS-CoV-2 since 2020
Twitter: AngieSHinrichs
Location: California
Blog: http://genome.ucsc.edu/
Pipeline components for real-time phylodynamic analysis
Conda recipes for the bioconda channel.
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.
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 provides functions to parse and compare the equivalency of variant strings described according to Human Genome Variation Society (HGVS) syntax.
RSV-A lineage definitions and proposals
Updates and details of monkeypox virus lineages designations
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.
science project: find gene clusters for various window sizes, compute avg neighborhood correlation & p-values
Repository for suggesting new lineages that should be added to the current scheme
Store of the trained model for pangolin to access.
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
The latest lineage assignments from pangolin.
Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
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.
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.
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
Global phylogenies of SARS-CoV-2 sequences
Ultrafast Sample Placement on Existing Trees
docs holder for usher wiki
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