wtdbg2

A haplotype-resolved assembler for accurate Hifi reads.

Deep-learning germline small-variant caller for long-read sequencing (PacBio HiFi/ONT) combining fast pileup calling with haplotype-resolved full-alignment calling; widely adopted as a standard in the Human Pangenome Reference Consortium production pipelines and PrecisionFDA truth challenges, with pre-trained models for multiple sequencing platforms, bioconda/Docker distribution, and a companion Clair-skills agent plugin for Claude Code/Codex (HKU-BAL, 394+ stars, BSD-3-Clause, actively maintained)

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

Nallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.