Stars
Genome modeling and design across all domains of life
Biological foundation modeling from molecular to genome scale
Transformer-based sequence correction method for genome assembly polishing
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Location of public benchmarking; primarily final results
minimizer-space de Bruijn graphs (mdBG) for whole genome assembly
PacificBiosciences / DevNet
Forked from ccano/DevNetThe DevNet project on github stores the PacBio DevNet website.
GIAB pipeline for benchmarking genome assemblies
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
Code examples of fast and simple k-mer counters for tutorial purposes
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Implicit Interval Tree with Interpolation Index
Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data
Calling deletions using deep convolutional neural
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
Python and C++ code for reading and writing genomics data.
DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG
Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
AndrewCarroll / mascp-jstools
Forked from hirenj/mascp-jstoolsJavascript widgets and tools for manipulating MASCP data