What are some good examples of well-engineered bioinformatics pipelines?

• gatk4-genome-processing-pipeline-azure

  4 7 0.0 wdl

  Workflows used for processing whole genome sequence data + germline variant calling.

  

• trinityrnaseq

  6 807 2.8 Perl

  Trinity RNA-Seq de novo transcriptome assembly

  

• 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.

  

• juicer

  1 393 0.0 Shell

  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments (by aidenlab)

  

• seqkit

  3 1,220 8.5 Go

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

Seqkit - thoroughly maintained with extensive tutorials and benchmarking info - https://github.com/shenwei356/seqkit

• spades

  4 684 9.4 C++

  SPAdes Genome Assembler

  

• sage

  5 198 7.7 Rust

  Proteomics search & quantification so fast that it feels like magic (by lazear)

You could check out https://github.com/lazear/sage - it's a near comprehensive program/pipeline for analyzing DDA/shotgun proteomics data. Most proteomics pipelines consist of running multiple, separate tools in sequence (search, spectrum rescoring, retention time prediction, quantification), but sage performs all of these. This cuts down on the need for disk space for storing intermediate results (none required), the need for IO (files are read once), and results in a proteomics pipeline that is >10-1000x faster than anything else, including commercial solutions

• rnaseq

  14 794 9.3 Nextflow

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  

• SaaSHub

  www.saashub.com featured

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

  

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