Arafat Rahman

Tag: Bioinformatics

  • Microbial ortholog gene clustering using real-dataset

    Microbial ortholog gene clustering using real-dataset

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    — 23 reads

    Once we assembled and annotated bacterial genomes, next step after inferring phylogeny usually is to finding and clustering orthologous genes. What are orthologs? Well, Genetics 101 tells us that they are genes evolutionary shared between multiple taxa descended from common ancestors. That means a series of (pretty-much) reliable replications and cell division passed between these…

  • Deciding how to construct a phylogenetic tree

    Deciding how to construct a phylogenetic tree

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    — 3 reads

    For any microbiology project, constructing a phylogenetic tree is an important analysis. A confusing one too — because there are many decisions to make along the way. These decisions can be both technical and hypothesis-driven. How to Build a Dataset for Phylogeny Let’s say someone has isolated and sequenced a few microbial strains. The most…

  • Annotation of Bacterial Genomes

    Annotation of Bacterial Genomes

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    — 35 reads

    This is Part 5 of tutorial series: NGS Workflow for Genome Assembly to Annotation for Hybrid Bacterial Data  We’ll be use hybrid sequencing data (Illumina and Nanopore). This tutorial has five parts.  Disclaimer: This post is a work in progress. This is genome assembly and annotation workflow that I use for microbial genomics. Previously, I used…

  • Hybrid Assembly of Bacterial Genome

    Hybrid Assembly of Bacterial Genome

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    — 29 reads

    This is Part 4 of tutorial series: NGS Workflow for Genome Assembly to Annotation for Hybrid Bacterial Data  We’ll be use hybrid sequencing data (Illumina and Nanopore). This tutorial has five parts.  Disclaimer: This post is a work in progress. This is genome assembly and annotation workflow that I use for microbial genomics. Previously, I used…

  • Microbial De Novo Genome Assembly from Long-Read Data

    Microbial De Novo Genome Assembly from Long-Read Data

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    in ,

    — 34 reads

    This is Part 3 of tutorial series: NGS Workflow for Genome Assembly to Annotation for Hybrid Bacterial Data  We’ll be use hybrid sequencing data (Illumina and Nanopore). This tutorial has five parts.  Disclaimer: This post is a work in progress. This is genome assembly and annotation workflow that I use for microbial genomics. Previously, I used…

  • Microbial De Novo Genome Assembly from Short-Read Data

    Microbial De Novo Genome Assembly from Short-Read Data

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    in ,

    — 50 reads

    This is yet another tutorial on microbial genome assembly. This is actually the Part 2 of tutorial series: NGS Workflow for Genome Assembly to Annotation for Hybrid Bacterial Data  In this series we’ll be use hybrid sequencing data (Illumina and Nanopore). This tutorial has five parts.  Part 1: Downloading and preparing data Part 2: Assembly with…

  • Programmatically Downloading Raw Data from NCBI

    Programmatically Downloading Raw Data from NCBI

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    in ,

    — 42 reads

    This is part of tutorial series: NGS Workflow for Genome Assembly to Annotation for Hybrid Bacterial Data We’ll be use hybrid sequencing data (Illumina and Nanopore). This tutorial has five parts. Disclaimer: This post is a work in progress. This is genome assembly and annotation workflow that I use for microbial genomics. Previously, I used…

  • বাংলায় জৈবতথ্যবিজ্ঞান চলবে কি?

    বাংলায় জৈবতথ্যবিজ্ঞান চলবে কি?

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    — 2 reads

    বিজ্ঞানে বিশেষায়িত ইংরেজী শব্দের পরিভাষা করা উচিত কি না তা নিয়ে বিস্তর বিতর্ক রয়েছে। বাংলাদেশে প্রধানমত হলো, না, পরিভাষা যেমন আছে তেমনই থাক, উচ্চতর শিক্ষা ইংরেজী ভাষাতেই থাকুক। চার বছরের স্নাতকের পড়াশুনায় যেসব শব্দ ইংরেজীতে অভ্যস্ত হয়েছি তাকে বাংলা করার কি দরকার? হাস্যকর শোনাবে তো। আপাতত এই বিতর্ককে পাশ কাটিয়ে বায়োইনফরমেটিক্সকে বাংলায় জৈবতথ্যবিজ্ঞান হিসেবেই লিখি।…

  • Creating a Publication Quality Phylogeny Using ggtree

    Creating a Publication Quality Phylogeny Using ggtree

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    — 1,230 reads

    A decade ago, circa 2012-2013, I used MEGA5 to infer phylogeny using simple Neighbour-Joining methods, and used the figure generated by MEGA5 to present and publish my results. Later, when I started learning other phylogeny reconstruction methods like Maximum Likelihood (ML) and Bayesian (which does not draw the tree for you), I started to explore…