A versatile pairwise aligner for genomic and spliced nucleotide sequences

Pangenome-based genome inference

Sequence-to-graph mapper and graph generator

tools for working with genome variation graphs

De novo assembler for single molecule sequencing reads using repeat graphs

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A single molecule sequence assembler for genomes large and small.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

Tool for globally phasing diploid assembly graphs with orthogonal data

PEPPER-Margin-DeepVariant

Read-based phasing of genomic variants, also called haplotype assembly

Basecalling configuration prediction through FASTQ files

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Get, parse, and extract information from the SRA metadata files

The buttery eel - a slow5 guppy/dorado basecaller wrapper

A complete diploid human genome

Fast and accurate coordinate conversion between assemblies

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Limma in Python

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

Illumina Human Methylation EPIC annotation to use with IlluminaHumanMethylationEPICB5manifest and minfi

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.