sam2interval
github.com/galaxyproject/tools-devteamA Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.
Sourced from
- bio.tools — snpfreq
- bio.tools — sam2interval
- GitHub — github.com/galaxyproject/tools-devteam
Related resources
Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF.
Python library for blazing-fast genomic interval operations and genomic file formats I/O on Polars DataFrames
Pan.bio is a cloud genomics platform for pipeline execution, exploratory analysis, and clinical variant interpretation. Workflows runs validated Nextflow and nf-core pipelines including Sarek, rnaseq, scrnaseq, mag, ampliseq, chipseq and atacseq without local installation. Notebooks provides Python and R sessions with a preinstalled bioinformatics stack, importing public data from GEO, SRA and IPG by accession and reading Workflows outputs directly. VAIC applies ACMG/AMP variant classification with gene-specific rule sets from CanVIG-UK and ClinGen ENIGMA, with automated evidence criteria implemented for BRCA1 and BRCA2. Cohorts provides federated analysis of patient data within a Trusted Research Environment.
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.
Deep learning-based variant caller