640 Open source projects that are alternatives of or similar to gawn

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Toolkit for preparing genomes for submission to NCBI

Earl Grey: A fully automated TE curation and annotation pipeline

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

🔬 BEDOPS: high-performance genomic feature operations

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

Example client programs for Saphetor's VarSome annotation API

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Extensive de-novo TE Annotator

Data intensive science for everyone.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

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

Analysis pipelines for sequencing data

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Track translations and automate workflow.

Pipelines using goroutines

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

Tools for constructing simple make-like pipelines in R.

Easy genetic ancestry predictions in Python

Forecast stock prices using machine learning approach. A time series analysis. Employ the Use of Predictive Modeling in Machine Learning to Forecast Stock Return. Approach Used by Hedge Funds to Select Tradeable Stocks

Functional Pipeline in Go

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

A platform for running XProc pipelines as web applications in a Java servlet container

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Railway oriented programming in Ember

Seven Bridges Genomics aligner/caller debugging and analysis tools

An Open Source Serverless Platform

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Snakemake based pipeline for RNA-Seq analysis

🏭 PDF text extraction pipeline: self-hosted, local-first, Docker-based

Genomics Workflows on AWS

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

xHLA: Fast and accurate HLA typing from short read sequence data

Java tools, helper, common utilities. A replacement of guava, apache-commons, hutool

Sort files in stream by path or any custom sort comparator

A WGS de novo assembler based on the FMD-index for large genomes

Short course on the targets R package

Build and deploy a serverless data pipeline on AWS with no effort.

🤖🎩assume-role-arn allows you to easily assume an AWS IAM role in your CI/CD pipelines, without worrying about external dependencies.

High performance transport protocol for distributed applications.

Collection of auditory models.

simuG: a general-purpose genome simulator

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

Find target sites for the miRNAs in genomic sequences

The magic message bus

A DNA Sequence Alignment/Map (SAM) library for Clojure

A tool for fast and accurate summarizing of variant calling format (VCF) files

This repo is no longer updated. Please see https://github.com/Autodesk/maya-usd

MorphL Community Edition uses big data and machine learning to predict user behaviors in digital products and services with the end goal of increasing KPIs (click-through rates, conversion rates, etc.) through personalization

Python package and CLI for whole-genome duplication related analyses

Generalised and highly customisable, hybrid-parallelism, database based, deep learning framework.

Cycle-accurate pre-silicon simulator of RISC-V and MIPS CPUs

An optimized docker image includes Android, Kotlin, Flutter sdk.