Finding Prophages in Bacterial Genomes – Step-by-Step
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) …
Step by Step: Completeness and Contamination of MAGs
This article demonstrates STEP by STEP checkm tutorial on how to estimate completeness and contamination of Metagenome Assembled Genomes (MAGs)
Bioconda: The Easiest Way to Install ANY Bioinformatics Tool
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 …
Easy BAM Sort with samtools sort
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 …
Pain-free Genome Depth Plotting
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 …
Remove Poor Reads in FASTQ/A
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 …