genome-analysis

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Long read / genome alignment software

Randomly subsample sequencing reads to a specified coverage

De novo genome assembly and multisample variant calling

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Long-reads Gap-free Chromosome-scale Assembler

Earl Grey: A fully automated TE curation and annotation pipeline

Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure

non-redundant, compressed, journalled, file-based storage for biological sequences

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

Scripts and procedures for detecting positively selected genes and codons in primates

Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

An Efficient Swiss Army Knife for Population Genomic Analyses in R

Fast Bayesian Hidden Markov Model with Wavelet Compression

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category