JosephLalli/gbwt
Substring index for paths in a graph
MD/PhD student at UWisc-Madison. I enjoy thinking about how ACGTs change, and what those changes do. Currently applying to Psychiatric residency programs.
Repositories
JosephLalli/xg
xg0: a simpler xg index
JosephLalli/libbdsg
Optimized sequence graph implementations for graph genomics
JosephLalli/vg
tools for working with genome variation graphs
JosephLalli/gcsa2
BWT-based index for graphs
JosephLalli/panCollapse
JosephLalli/CIGMA
JosephLalli/brainvar-counterfactual-methods
Versioned methods for the BrainVar GRCh38 and T2T counterfactual reproduction
JosephLalli/shapeit5
Segmented HAPlotype Estimation and Imputation Tool
JosephLalli/phasing_T2T
Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.
JosephLalli/LiftoverIndel
Tool to liftover variants between references in an indel-aware manner
JosephLalli/tensorqtl
Ultrafast GPU-based QTL mapper
JosephLalli/Brainvar2_wgs
Reproducible BrainVar2 GRCh38 whole-genome germline variant-calling workflow
JosephLalli/brainvar2_mbv
Portable BrainVar and BrainVar2 QTLtools MBV sample-matching workflow and decision documentation
JosephLalli/pywfa
Python wrapper for wavefront alignment using WFA2-lib
JosephLalli/vcfdist
vcfdist: Accurately benchmarking phased variant calls
JosephLalli/codex-swarm-env
Codex-native multi-agent development environment scaffold for multiSHAPE
JosephLalli/multiSHAPE
multiSHAPE is an extension of SHAPEIT4/5 to simultaneous biallelic and multiallelic genotype phasing.
JosephLalli/ebay_photo_hosting
JosephLalli/atacseq
ATAC-seq peak-calling and QC analysis pipeline
JosephLalli/mvsusieR
A new model and algorithm for multivariate Bayesian variable selection regression.
JosephLalli/shapeit5_old
Segmented HAPlotype Estimation and Imputation Tool
JosephLalli/sarek_pangenome
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
JosephLalli/sarek_old
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
JosephLalli/sarek_archive
Archived copy of old sarek fork
JosephLalli/biastools
Tool to calculate allelic bias in aligned, variant called sequencing datasets
JosephLalli/ENCODE-cCREs
Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
JosephLalli/str-analysis
Scripts and utilities for analyzing tandem repeats (TRs).
JosephLalli/personalized_rnaseq
JosephLalli/PiMaker
Tool to calculate nucleotide diversity statistics in large pooled population datasets