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

Easy NCBI Genome Download

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NCBI genome download can be a very unpleasant job. This page shows how to use ncbi-genome-download to easily download NCBI genomes with a single command line.

Bioinformatics

Fast Conversion of Lowercase Sequences to Uppercase in FASTA Format

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This tutorial teaches two approaches to convert lowercase to uppercase sequences in FASTA format. In bioinformatics, a FASTA with lowercase bases implies that regions are low …

Bioinformatics

Quick Sequencing Depth and Coverage Check

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This tutorial teaches how to run a quick sequencing depth and coverage check for one or more reference sequences.

Bioinformatics

The Fastest Way to Read a FASTA in Python

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This tutorial teaches a fast approach on how to read sequences from large FASTA files in Python using Pysam.

Bioinformatics

Multiple Sequence Alignment – Theory and Practice – Step-by-Step

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This blog post described Multiple Sequence Alignment (MSA) focusing on the theory and practice – Step-by-Step using MAFFT and Muscle.

Bioinformatics

The Easiest Way to Download Genomic Data from NCBI SRA, MG-RAST, etc

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This tutorial will teach you how to download NGS data and metadata from repositories such as NCBI SRA, MG-RAST, Imicrobe, etc – very helpful to download …

Bioinformatics

Fun Fact: What is so special about an odd k-mer length?

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Have you noticed that most assemblers use an odd k-mer length? Do you know why? Don’t you think it is odd? This blog post explains below …

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, …