This recipe demonstrates the basic use of Entrez Direct from the command line
This script was written in class to demonstrate the process of refactoring code one step at a time.
This recipe performs data quality control on FASTQ data downloaded from SRA.
This recipe performs data quality control with the tool cutadapt on microRNA FASTQ data downloaded …
This recipe demonstrates the use of BLAST to identify a viral sequence.
This recipe demonstrates the utility of blast databases for manipulating sequences.
This recipe demonstrates the creation of custom nucleotide and protein databases.
This recipe demonstrates the use of the BWA short read aligner to create a BAM file.
This recipe demonstrates the use of the BOWTIE short read aligner to create a BAM file.
This recipe is a Makefile that executes the bwa and bbmap aligners.
Evaluate a genome assembly
Visualizing large scale genomic variations in short read data.
This recipe follows the variant calling process in the Biostar Handbook.
This recipe demonstrates variant calling using freebayes on simulated data.
The following is based on a homework assignment submitted for the Applied Bioinformatics course.
Variant miscalling demonstration
Bacterial variant caller
Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in …
Half-sequence and half mythical-beast, "unaligned" BAM files are used to store FASTQ files.
RNA-Seq differential expression with alignments and using different statistical methods.
This recipe performs an RNA Seq analysis using kallisto.
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