286 Open source projects that are alternatives of or similar to kover

phenol: Phenotype ontology library

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Improve the quality of a denovo assembly by scaffolding and gap filling

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Predict AMPs in (meta)genomes and peptides

Bead-based single-cell atac processing

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Examples to get started with IBM Functional Genomics Platform

WebAssembly modules for genomics

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A package for designing activity-informed nucleic acid diagnostics for viruses.

Python-based UCSC genome browser snapshot-taker and gallery-maker

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

A compressed, associative, exact, and weighted dictionary for k-mers.

Grammar of Scalable Linked Interactive Nucleotide Graphics

Explore rearrangements and copy-number amplifications in a cancer genome

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

A fast tool for hybrid genome assembly of long and short reads

find large indels (in the blind spot between GATK/freebayes and SV callers)

Analysing Capture Seq Count Data

Identify phage regions in bacterial genomes for masking purposes

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Curated List of Biomarkers, Blood Tests, and Blood Tracking

Tools for analyzing 10X Genomics data

Transcripts annotation and GO enrichment Fisher tests

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Bioconductor package for management of multi-assay data

interactive Multi Objective K-mer Analysis

Nextflow basic tutorial for newbie users

Command line utility for manipulating Illumina-generated FastQ files.

Big Compute Learning Labs

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

A library for manipulating bioinformatics sequencing formats in Apache Spark

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

A phenotype-based tool for variant prioritization in WES and WGS data

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Forward-time simulation in Python using fwdpp

Multilocus sequence typing by blast using the schemes from PubMLST

Resource of human chromosome schematics & images

Explore gnomAD datasets on the web

🐳 Bio-dockers: dockerized bioinformatic tools

Ultrafast sequence typing and gene detection from NGS raw reads

Internationalisation of the HPO content

Manhattan plot Generator

Numerical Encoding for Human Genetic Variants

CUT&RUN and CUT&Tag data processing and analysis

A fast, scalable, and accurate local ancestry method.

Introduction to the Command Line for Genomics

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

mgatk: mitochondrial genome analysis toolkit

Interactive assembly and analysis of RAD-seq data sets

An R framework for phylostratigraphy

A tool to plot significant regions of GWAS