578 Open source projects that are alternatives of or similar to unimap

A tool to circularize genome assemblies

Proof-of-concept seq-to-graph mapper and graph generator

GenomeTools genome analysis system.

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Code examples of fast and simple k-mer counters for tutorial purposes

A package for designing compact and comprehensive capture probe sets.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Fast hash function for DNA sequences

Assembling the cause of phenotypes and genotypes from NGS data

Provide R access to the NCI Genomic Data Commons portal.

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

GCP Essentials for Bioinformatics Researchers

De novo assembly based variant calling pipeline for Illumina short reads

BACNET is a Java based platform to develop website for multi-omics analysis

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Earl Grey: A fully automated TE curation and annotation pipeline

annotate a VCF with other VCFs/BEDs/tabixed files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A high-performance, Pythonic language for bioinformatics

A fast 23andMe genome text file parser, now superseded by arv

Ultra-fast and memory-efficient (meta-)genome assembler

Java utilities for Bioinformatics

Python library to facilitate genome assembly, annotation, and comparative genomics

Efficient pythonic random access to fasta subsequences

Scripts to download genomes from the NCBI FTP servers

Tools to process and analyze deep sequencing data.

Toolkit for preparing genomes for submission to NCBI

A cool place to store your Hi-C

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

A collection of publications on comparison of high-throughput sequencing technologies.

An interactive web tool for quality control of DNA sequencing data

Flexible genotype query among 30,000+ samples whole-genome

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Antimicrobial Resistance Identification By Assembly

Data intensive science for everyone.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

JavaScript VisualizationTools

A faster lmm for GWAS. Supports GPU backend.

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.

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

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

Clustering scRNAseq by genotypes

Predict AMPs in (meta)genomes and peptides

Forward-time simulation in Python using fwdpp

Explore rearrangements and copy-number amplifications in a cancer genome

Resource of human chromosome schematics & images

phenol: Phenotype ontology library

Bead-based single-cell atac processing

A proof of concept of RNAseq pipeline

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

Explore gnomAD datasets on the web

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

A fast, scalable, and accurate local ancestry method.