Beast code in Giters

Andrew Carroll's starred repositories

evo

Biological foundation modeling from molecular to genome scale

Language:Jupyter NotebookApache-2.087400

GLnext

Scalable gVCF merging and joint variant calling

Language:KotlinApache-2.0500

deeppolisher

Transformer-based sequence correction method for genome assembly polishing

Language:Jupyter NotebookBSD-3-Clause2200

HiFi-human-WGS-WDL

Language:WDLBSD-3-Clause-Clear4500

deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

BSD-3-Clause9600

pepper

PEPPER-Margin-DeepVariant

Language:PythonMIT23000

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Language:PythonBSD-3-Clause21800

CSL_public_benchmark

Location of public benchmarking; primarily final results

Language:ShellApache-2.01800

rust-mdbg

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

Language:RustMIT17400

DevNet

The DevNet project on github stores the PacBio DevNet website.

11300

genomics-research

Language:Jupyter Notebook11400

HPP_Year1_Data_Freeze_v1.0

4600

giab-asm-benchmarking

GIAB pipeline for benchmarking genome assemblies

Language:JavaScriptNOASSERTION700

WFA-paper

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

Language:CNOASSERTION19900

GenomicSQLite

Genomics Extension for SQLite

Language:C++Apache-2.015600

kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

Language:C++MIT16100

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Language:C++MIT50400

SDA

Segmental Duplication Assembler (SDA).

Language:PythonMIT4200

iitii

Implicit Interval Tree with Interpolation Index

Language:Jupyter NotebookApache-2.04100

bwa-mem2

The next version of bwa-mem

Language:C++NOASSERTION69800

sv-benchmark

Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data

4200

DeepSV

Calling deletions using deep convolutional neural

Language:Python2300

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Language:PythonApache-2.010200

Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Language:PythonBSD-3-Clause17100

nucleus

Python and C++ code for reading and writing genomics data.

Language:C++NOASSERTION77600

DCNet

DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG

Language:Jupyter Notebook6900

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

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fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Language:C++MIT182200

mascp-jstools

Javascript widgets and tools for manipulating MASCP data

Language:JavaScript100

elysia

Elysia brain simulation

Language:JavaScriptBSD-3-Clause100