273 Open source projects that are alternatives of or similar to Assemblytics

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

Examples to get started with IBM Functional Genomics Platform

Numerical Encoding for Human Genetic Variants

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

ntHash implementation in Rust

Multilocus sequence typing by blast using the schemes from PubMLST

Bead-based single-cell atac processing

A tool to plot significant regions of GWAS

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

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

GA4GH Variation Representation Python Implementation

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

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.

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

Explore rearrangements and copy-number amplifications in a cancer genome

🐳 Bio-dockers: dockerized bioinformatic tools

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

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

Analysing Capture Seq Count Data

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

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

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

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

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

Bioconductor package for management of multi-assay data

A secure encryption tool for genomic data

Command line utility for manipulating Illumina-generated FastQ files.

Nextflow basic tutorial for newbie users

Resource of human chromosome schematics & images

Big Compute Learning Labs

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

Tools for analyzing 10X Genomics data

Forward-time simulation in Python using fwdpp

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

phenol: Phenotype ontology library

A fast, scalable, and accurate local ancestry method.

Explore gnomAD datasets on the web

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

Ultrafast sequence typing and gene detection from NGS raw reads

Grammar of Scalable Linked Interactive Nucleotide Graphics

Manhattan plot Generator

Identify phage regions in bacterial genomes for masking purposes

CUT&RUN and CUT&Tag data processing and analysis

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

Introduction to the Command Line for Genomics

Spark VCF data source implementation for Dataframes

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

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 bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

WebAssembly modules for genomics

simple viewer for variant call format using htslib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Transcripts annotation and GO enrichment Fisher tests

Interactive assembly and analysis of RAD-seq data sets

An R framework for phylostratigraphy

Predict AMPs in (meta)genomes and peptides

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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