shlokanegi

Shloka Negi's starred repositories

ErrorSimulator_UShER_SARSCoV2

A simulation platform that tries incorporating realistic errors into simulated SARS-CoV-2 genomes.

Language:Python300

MeOW

Automated Detection and Qualification of Differential Methylation

Language:RGPL-3.01000

hprc_intermediate_assembly

Language:ShellMIT100

modkit

A bioinformatics tool for working with modified bases

Language:RustNOASSERTION12100

HG002-issues

HG002 human reference genome issue tracking and polishing

1000

napu_wf

WDL workflows for variant calling and assembly using ONT

Language:WDLNOASSERTION2700

card_nanopore_wf

WDL variant calling workflows

100

variant_annotation_wf

Workflow to annotate SNVs, indels, and structural variants

Language:PythonMIT100

phastSim

fast sequence evolution simulation for SARS-CoV-2 and similar

Language:PythonGPL-3.01600

BTE

Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit

Language:CythonMIT1000

hap.py

Haplotype VCF comparison tools

Language:C++NOASSERTION40200

vg

tools for working with genome variation graphs

Language:C++NOASSERTION108200

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language:PythonBSD-3-Clause313500

sequenceTubeMap

displays multiple genomic sequences in the form of a tube map

Language:JavaScriptMIT17700

HG002

A complete diploid human genome

8400

remora

Methylation/modified base calling separated from basecalling.

Language:PythonNOASSERTION14900

CHM13

The complete sequence of a human genome

NOASSERTION88800