Powerful statistics for VCF files

k-mer based assembly evaluation

Iterate over minimizers of a DNA sequence

compacted de Bruijn graph construction in low memory

software tools for haplotype assembly from sequence data

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

A genome visualization python package for comparative genomics

Ultra-fast preprocessing and quality control for long-read sequencing data

Correcting errors in noisy long reads using variation graphs

Signal-level algorithms for MinION data

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

Graph-based assembly phasing

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

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

MEME motif-based sequence analysis tools (http://meme-suite.org), with FreeBSD tweaks

Biological sequence analysis for the modern age.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Aligns short reads using dynamic seed size with strobemers

DMRs detection, annotation and analysis

Versatile open-source tool for microbiome analysis

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

AdapterRemoval v2 - rapid adapter trimming, identification, and read merging

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

Classifiers trained on commonly used variable regions of Prokaryotic 16S rRNA genes

Pod5: a high performance file format for nanopore reads.

Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

Differential abundance (DA) and correlation analyses for microbial absolute abundance data