Category: Bioinformatics

This page contains short Bioinformatics tutorials. However, very informative on the basics needs for someone learning the topic, and tricks for someone more experienced. The posts target bioinformatics with python, definition, jobs, sequencing, metagenomics analysis, samtools, etc.

Bioinformatics

Estimate Genome Size and Best k-mer Size for Assembly – Step-by-Step

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This tutorial shows how you can estimate the genome size and the best k-mer length for genome assembly using KmerGenie. Moreover, the tutorial shows how to …

Bioinformatics

Reference-Free Metagenomic Datasets Comparison – Step-by-Step

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Reference-free metagenomic methods are very useful to compare datasets with high levels of unknown sequences. This tutorial teaches how this can be done going from metagenomic …

Bioinformatics

Painless Prokaryote Pan Genome – Step-by-Step

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This tutorial shows how to annotate genomes in FASTA format and how to generate the pan-genome and core genome using the annotation. For annotating the genes, …

Bioinformatics

How to Simulate NGS reads – Step-by-Step

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This tutorial shows how to use a read simulator in Next-Generation Sequencing (NGS) sequence for single-cell genomes and metagenomics. It covers how to simulate Illumina (NovaSeq, …

Bioinformatics

Genome Assembly for Omics – Step-by-Step

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This tutorial will show step-by-step how to assembly single-cell Microbial genomes and metagenomic datasets. Here we will be using SPAdes to assemble the datasets and show …

Bioinformatics

Painless Metagenomic Contigs Binning – Step-by-Step

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This blog post teaches a step-by-step on binning metagenomic contigs using two unsupervised methods – CONCOCT and Metabat2. Furthermore, it uses a simulated metagenomic to evaluate …

Bioinformatics

Everything About the NCBI BLAST Aligner and Faster Alternatives

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This blog post talks about everything you need to know about BLAST (Basic Local Alignment Search Tool) NCBI. Here you will learn: How to run it …

Bioinformatics

Scaffolding Genome: Increase Draft Genome N50 Length – Step-by-Step

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This tutorial demonstrates how to increase a draft genome N50 by using Scaffold_Builder which takes pre-assembled genomes and a closely related reference genome.

Bioinformatics

1,000 Fold Speed up on Metagenomic Functional Profile

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Would you believe that you could estimate the functional profile for your metagenomic dataset 1,000 times faster than other tools out there? In this tutorial, I …

Bioinformatics

Finding Prophages in Bacterial Genomes – Step-by-Step

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This tutorial presents a step-by-step on finding prophages (phage) in bacterial genomes from a FASTA file (not Genbank format) to another FASTA with the (if any) …