Jul 20, 2023

Efficient clustering and assembling of short reads, especially for RAD

Rainbow provides an ultra-fast and memory-efficient solution to clustering and assembling short genetic sequence reads produced by Restriction site Associated DNA Sequencing RAD-seq. It does this by, first, clustering reads using a spaced seed method, then it divides potential groups into haplotypes in a top-down manner. Next, along a guide tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Both optimal and suboptimal assembly results are output.

FreeBSD port “rainbow” falls in the category of biology that is explicitly designed to support bioinformatics applications. The introduction of the rainbow software port in FreeBSD has made complex bioinformatics workflows simpler and more efficient.

Introduction to FreeBSD and Ports

FreeBSD is one of the most popular open-source operating systems. The FreeBSD ports collection offers a simple way for users and developers to install and manage a vast array of applications. Essentially, Ports are a collection of files that provide the instructions needed to compile and install applications. This is especially beneficial for those who desire a personalized system with applications tailored specifically to their needs.

One such intriguing port is the “rainbow” port in the category of biology.

What is the Rainbow port?

Rainbow is an ultra-fast and memory-efficient short-read assembler for large-scale genomics, primarily used for processing next-generation DNA sequencing data. You can learn more about the rainbow port [here]https//freebsdsoftware.org/biology/rainbow.html.

Installing the Rainbow Port

Here is a simple set of instructions on how to install the rainbow port

  • First, you need to update the ports tree using command portsnap fetch update
  • Then within the terminal, navigate to the directory of the port using cd /usr/ports/biology/rainbow/
  • To install the port, execute make install clean

Rainbow port software is now installed on your FreeBSD system and ready to use.

Working with Rainbow Port

To run the Rainbow port, the general command line syntax is as follows

rainbow [options] <reads.fq> 

This command a number of files depending on the options selected.

With the help of different options, users can adjust the parameters depending on the complexity and requirements of their needs. Here are some of the useful rainbow options

-1 Generate the clusters only.

-2 Generate the consensus reads.

-3 Generate the final contig sequences.

Benefits of Using Rainbow Port

The uniqueness of Rainbow comes with its usage and the benefits it offers. Here are a few benefits

  • It’s highly efficient in terms of computational resources.
  • It supports complex bioinformatics workflows which helps in the analysis of genomic sequences.
  • It’s especially helpful for large-scale de novo transcriptome assembly with short-read RNA-Seq data.
  • Rainbow port offers higher-quality consensus sequences.
  • It proves highly efficient for those who need to assemble very large genomes from short reads.


Rainbow port is a powerful and highly efficient tool for any researcher in the field of bioinformatics. Its seamless integration into FreeBSD makes it a valuable addition to the biological software resources available through open source.

Other than Rainbow, FreeBSD hosts a rich collection of ports that can cater to diverse needs. In fields like IT security, ports like nmap can be highly valuable. You can learn more about nmap [here]https//freebsdsoftware.org/security/nmap.html.

Remember, the underlying strength of FreeBSD lies in its extensive collection of ported software. Therefore, always keep an eye on the updates and improvements in FreeBSD ports collections.

To explore more about FreeBSD and its ports, visit the official FreeBSD website. FreeBSD ports offer a realm of possibilities to customize your FreeBSD system.

To sum up, this blog post provides a brief manual on using the FreeBSD port Rainbow in bioinformatics. We believe it will help both new and experienced FreeBSD users to utilize this efficient tool for genomic sequence analysis. Experiment with the Rainbow port on your FreeBSD system, and observe the profound impact it can have on your bioinformatics workflows. Happy FreeBSDing!

Note Always ensure you’re using an up-to-date FreeBSD system and have the latest version of your desired port to ensure efficiency and security. Make sure to follow the official FreeBSD resources and documentation where you can get detailed and technical explanations.

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data