Shloka Negi's repositories
ErrorSimulator_UShER_SARSCoV2
A simulation platform that tries incorporating realistic errors into simulated SARS-CoV-2 genomes.
DNAModsWRemora
Evaluating Remora for Identification of DNA mods
callmods_5hmC
Generates high-confidence 5hmC mod calls using modkit, other stats and plots
card_nanopore_wf
WDL workflows for variant calling and assembly using ONT
denovo_snps
Workflow built over vcfeval with custom-filtering to generate annotated denovo candidates in a trio.
GiraffeDeepVariant_Exome
Performance Evaluation of Giraffe-DeepVariant Workflow on WES data
intro_python
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
variant_annotation_wf
Workflow to annotate SNVs, indels, and structural variants
merge_VCFs_wf
Merge individual sample VCFs to create a unified multi-sample VCF, optionally allowing for modification of sample names.
modbam_calcMeth_wf
Calculates haplotype-specific average percent modification per region, and additional stats, using modbamtools
pb-motif
PB-Motif: A method for identifying gene/pseudogene rearrangements with PacBio long reads
wdl-workflows
WDL workflows
wdl_workflows
WDL workflows