284 Open source projects that are alternatives of or similar to hickit

Large genome reassembly based on Hi-C data, continuation of GRAAL

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

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

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Explore gnomAD datasets on the web

GA4GH Variation Representation Python Implementation

use the noise

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Big Compute Learning Labs

Manhattan plot Generator

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

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

phenol: Phenotype ontology library

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Nextflow basic tutorial for newbie users

DriverPower

Ultrafast sequence typing and gene detection from NGS raw reads

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Transcripts annotation and GO enrichment Fisher tests

CUT&RUN and CUT&Tag data processing and analysis

Finds SNP sites from a multi-FASTA alignment file

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Biopython Jupyter Notebook tutorial to characterize a small genome

A library for manipulating bioinformatics sequencing formats in Apache Spark

Introduction to the Command Line for Genomics

simuG: a general-purpose genome simulator

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

Explore rearrangements and copy-number amplifications in a cancer genome

simple viewer for variant call format using htslib

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

A secure encryption tool for genomic data

Bead-based single-cell atac processing

Genome-wide imputation pipeline

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

The GenePattern Server web application

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

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Examples to get started with IBM Functional Genomics Platform

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

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

a pileup library that embraces the huge

Analysing Capture Seq Count Data

Collection of scripts for bacterial genomics

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.

Genome Annotation Without Nightmares

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

Phage-Host Interaction Search Tool

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

High-performance error correction for Illumina resequencing data

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

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

Easy genetic ancestry predictions in Python

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

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Python package and CLI for whole-genome duplication related analyses

Docker for 4DN Hi-C processing pipeline

Spark VCF data source implementation for Dataframes

WebAssembly modules for genomics