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SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

kb-python is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows.

A tool to compress FASTQ files with ultra-high compression ratio and high speed. repaq supports compressing the FASTQ to .rfq or .rfq.xz formats. Compressing to .rfq is ultra fast, while compressing to .rfq.xz provides very high compression ratio.

dysgu (pronounced duss-key) is a set of command line tools and python-API, for calling structural variants using paired-end or long read sequencing data.

a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.

antiSMASH (antibiotics and Secondary Metabolite Analysis SHell) allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.

a utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data. It was written to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data.

a method for structural variations discovery from accurate long reads (e.g PacBio HiFi), based on the notion of sample-specific strings (SFS, or simply specific strings).