499 Open source projects that are alternatives of or similar to Khmer

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

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

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

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

Intuitive local web frontend for the BLAST bioinformatics tool

MView extracts and reformats the results of a sequence database search or multiple alignment.

A simplified pipeline for ctDNA sequencing data analysis

RAxML Next Generation: faster, easier-to-use and more flexible

A curated list of resources for machine learning for small-molecule drug discovery

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

List of Computer Science courses with video lectures.

A genome browser that shows long reads and complex variants better

Version 5 of the CAFE phylogenetics software

Deep learning infrastructure for bioinformatics

Phylogenetic trees in Julia

Toolset for SV simulation, comparison and filtering

Feature extraction algorithm for genomic data

🎯 Bloom filters for C++11

Go Client for RedisBloom probabilistic module

Rapid large-scale prokaryote pan genome analysis

🎯 Human transcription factor target genes.

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Annotated data.

A python wrapper for the benchling api

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Tools for working with SAM/BAM data

Syntax highlighting for computational biology

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

The sources of the openSNP website

De novo assembly based variant calling pipeline for Illumina short reads

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Next generation sequencing reads de novo assembler.

Modular and universal bioinformatics

R package for analyzing single-cell RNA-seq data

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

Package for fetching metadata and downloading data from SRA/ENA/GEO

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

parallel fastq-dump wrapper

Real-time species-typing visualisation for nanopore data.

Read DNA sequences from colourful Microsoft Word documents

个人工具汇总：一致性哈希工具，Bitmap工具，布隆过滤器参数生成器，Yaml和properties互转工具，一键式生成整个前后端工具，单机高性能幂等工具，zookeeper客户端工具，分布式全局id生成器，时间转换工具，Http封装工具

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

nim wrapper for htslib for parsing genomics data files

A Golomb Coded Set implementation in Rust

Simple simulation of single-cell RNA sequencing data

The Chemistry Development Kit

CoRA Docs

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Fast Bloom filter with concurrent accessibility, powered by :atomics module.

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Simple pure Python SAM parser and objects for working with SAM records

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

A cross-platform, efficient and practical CSV/TSV toolkit in Golang