Assembly and intrahost/low-frequency variant calling for viral samples
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Updated
May 9, 2024 - Nextflow
Assembly and intrahost/low-frequency variant calling for viral samples
CLI tool for flexible and fast adaptive sampling on ONT sequencers
Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq
ClairS - a deep-learning method for long-read somatic small variant calling
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)
MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics; MegaPath-Nano-Amplicon: filtering module for metagenomic amplicon data
FLAME: Full Length Adjecency Matrix Enumeration - is a module that allows for the analysis of ONT Nanopore RNA long-read sequencing data.
Analyses of Penter, Borji & Nagler et al., 2023
Get L. pneumophila ST from long-read or hybrid assemblies.
Build highly accurate transcripts from long-read RNA data
CatMOD is a CatBoost-based feature-concatenation model for RNA modification recognition from ONT DRS.
Benchmarking for long-reads assembler
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