Fast Conversion of Lowercase Sequences to Uppercase in FASTA Format
by: onestop_data
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 …
Quick Sequencing Depth and Coverage Check
by: onestop_data
This tutorial teaches how to run a quick sequencing depth and coverage check for one or more reference sequences.
The Fastest Way to Read a FASTA in Python
by: onestop_data
This tutorial teaches a fast approach to how to read sequences from large FASTA files in Python using Pysam. I know how reading large FASTA files …
Multiple Sequence Alignment – Theory and Practice – Step-by-Step
by: onestop_data
This blog post described Multiple Sequence Alignment (MSA) focusing on the theory and practice – Step-by-Step using MAFFT and Muscle.
The Easiest Way to Download Genomic Data from NCBI SRA, MG-RAST, etc
by: onestop_data
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 …
Fun Fact: What is so special about an odd k-mer length?
by: onestop_data
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 …
Estimate Genome Size and Best k-mer Size for Assembly – Step-by-Step
by: onestop_data
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 …
Reference-Free Metagenomic Datasets Comparison – Step-by-Step
by: onestop_data
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 …
Painless Prokaryote Pan Genome – Step-by-Step
by: onestop_data
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, …
How to Simulate NGS reads – Step-by-Step
by: onestop_data
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, …