Top 11 bioinformatics-pipeline Open-Source Projects

• scipipe

  1 1,052 3.0 Go

  Robust, flexible and resource-efficient pipelines using Go and the commandline

  

• reflow

  7 954 6.2 Go

  A language and runtime for distributed, incremental data processing in the cloud

  

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• bacalhau

  12 614 9.8 Go

  Compute over Data framework for public, transparent, and optionally verifiable computation

  

Project mention: Deno Cron | news.ycombinator.com | 2023-11-29

This is really interesting - we’ve tried really hard to solve some of these with Bacalhau[1] - a much simpler distributed compute platform. Would love your feedback!

[1] https://github.com/bacalhau-project/bacalhau

Disclosure: I confounded Bacalhau

• pysradb

  1 296 7.3 Python

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

• ariba

  1 154 3.0 Python

  Antimicrobial Resistance Identification By Assembly

  

• open-cravat

  1 106 8.9 JavaScript

  A modular annotation tool for genomic variants

  

• too-many-cells

  0 100 4.5 Haskell

  Cluster single cells and analyze cell clade relationships with colorful visualizations.

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

• edgecase

  1 14 2.1 Python

  A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

• GermlineMutationCalling

  1 12 0.0 Python

  An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

• drugfindR

  1 7 9.4 R

  Repository holding the code for the drugfindR R package

  

• Baltica

  1 7 2.6 R

  Baltica: integrated differential junction usage

  

bioinformatics-pipeline related posts

• [Tool] Germline variant calling pipeline using Snakemake

  1 project | /r/bioinformatics | 20 Sep 2021

• Novel Splice Variants in RNAseq Data

  1 project | /r/bioinformatics | 15 Sep 2021

• reflow - A language and runtime for distributed, incremental data processing in the cloud

  1 project | /r/DistributedComputing | 20 May 2021

• reflow - A language and runtime for distributed, incremental data processing in the cloud

  1 project | /r/Cloud | 20 May 2021

• reflow - A language and runtime for distributed, incremental data processing in the cloud

  1 project | /r/golang | 20 May 2021

• Reflow, a language for distributed, incremental data processing in the cloud

  1 project | news.ycombinator.com | 17 May 2021

• Jolie, the service-oriented programming language

  3 projects | news.ycombinator.com | 17 May 2021
• A note from our sponsor - SaaSHub
  www.saashub.com | 16 May 2024

  SaaSHub helps you find the best software and product alternatives Learn more →

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