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

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) …

Bioinformatics

Step by Step: Completeness and Contamination of MAGs

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This article demonstrates STEP by STEP checkm tutorial on how to estimate completeness and contamination of Metagenome Assembled Genomes (MAGs)

Bioinformatics

Bioconda: The Easiest Way to Install ANY Bioinformatics Tool

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How many times have you found an amazing bioinformatics tool but had trouble installing it into your personal computer/ server? This happened to me every week …

Bioinformatics

Metagenomic Taxonomic Profile in Seconds

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Would you believe if I tell you that you get a metagenomic taxonomic profile in seconds in your regular compute? If you don’t believe it, I …

Bioinformatics

The Easiest way to Calculate N50 for Genome Assembly

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This short tutorial demonstrates how you can use Python to compute N50 for Genome Assembly. What is N50? How to calculate N50 Is a larger n50 …

Bioinformatics

Easy BAM Sort with samtools sort

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This short tutorial demonstrates how samtools sort is used to sort BAM genomic coordinates. Moreover, how to pipe samtool sort when running bwa alignment, and how …

BioinformaticsData visualization

Pain-free Genome Depth Plotting

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A genome depth plot is a great way to visualize how well a target genome is covered across the genome. This can be used to eyeball …

Bioinformatics

Remove Poor Reads in FASTQ/A

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Have you needed to Clean your FASTA/FASTQ file? I know it is a common task. Back in the day, I found a Python 2 script to …

BioinformaticsData visualization

Effortless Recruitment Plot

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Creating a recruitment plot can be a pain when you don’t have the right tool. A fragment recruitment plot is a great way to visualize how …