DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
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Mar 11, 2025 - Python
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long-read-sequencing
Here are 46 public repositories matching this topic...
ClairS - a deep-learning method for long-read somatic small variant calling
bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads
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Nov 28, 2025 - Python
Graph-based assembly phasing
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Nov 25, 2025 - Python
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina snvs long-reads ont long-read-sequencing tumors tumor-only
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Nov 13, 2025 - Python
Long-read splice alignment with high accuracy
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Sep 26, 2024 - Python
Single cell Nanopore sequencing data for Genotype and Phenotype
gene-expression single-cell isoforms demultiplexing cell-barcode rna-seq-pipeline single-nucleotide-variation long-read-sequencing nanopore-analysis-pipeline umi-curation
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May 15, 2025 - Python
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
bioinformatics nanopore metagenomics pacbio microbial-genomics microbiome long-read-sequencing metagenome-assembled-genomes
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Oct 24, 2025 - Python
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
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Jan 18, 2023 - Python
Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
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Dec 15, 2025 - Python
Clair3-RNA - a long-read small variant caller for RNA sequencing data
rna-seq deep-learning nanopore rna variant-calling rna-editing rna-seq-pipeline ont long-read-sequencing pacbio-iso-seq
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Dec 23, 2025 - Python
Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
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Apr 26, 2025 - Python
NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)
bioinformatics pipeline dna-methylation nanopore-sequencing long-read-sequencing methylation-calling
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Dec 5, 2025 - Python
An algorithm for centromere assembly using long error-prone reads
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May 25, 2021 - Python
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
metagenomics metagenomic-analysis metagenomic-classification long-reads taxonomic-classification long-read-sequencing taxonomic-profiling
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Jul 23, 2025 - Python
Lightweight bioinformatics pipeline for microbial genome recovery
bioinformatics nanopore metagenomics pacbio microbial-genomics microbiome singularity-container snakemake-workflow long-read-sequencing metagenome-assembled-genomes
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Oct 23, 2025 - Python
A short tandem repeat (STR) genotyping and analysis toolkit for long reads
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Dec 15, 2025 - Python
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
bioinformatics genomics repeats bioinformatics-pipeline haplotypes genomics-visualization long-reads telomeres long-read-sequencing
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Jan 25, 2024 - Python
🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing
bioinformatics nanopore genomics python3 bioconda genome-analysis crispr-target long-read-sequencing
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Dec 11, 2025 - Python
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
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Dec 18, 2024 - Python
Coronavirus (SARS-Cov-2) sequencing analysis
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Oct 5, 2021 - Python
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