Octopus

Deep learning-based variant caller

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

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.

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)