This recipe compares alignment before and after QC using two different tools, bwa and bowtie2
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.
bwa
bbmap
The recipe generates simulated sequencing reads from NCBI accession numbers. It then performs class…
Evaluate a genome assembly
Visualizing large scale genomic variations in short read data.
This recipe evaluates the accuracy of the Kraken 2 classification for selected markers.
This recipe evaluates the accuracy of the Centrifuge classification for selected markers.
This recipe follows the variant calling process in the Biostar Handbook.
This recipe reads in fastq files and applies filtering & trimming parameters to clean the data.…
This recipe downloads sequencing data from an NCBI project.
This recipe downloads sequencing data from an SRA run.
DADA2 based data analysis.
This recipe runs eDNAoccupancy R package to estimate the occurrence of a species by modeling eDNA d…
This recipe demonstrates variant call generation for several samples at once.
This recipe demonstrates variant call generation from sequencing deposited at SRA
This recipe prints: Hello World!
This recipe demonstrates a bacterial variant caller with minimap2 and bcftools
This is the simplest possible recipe.
This recipe performs an RNA Seq analysis of the Zika data using an alignment based method
This recipe performs an RNA Seq analysis of the Zika data using a classification based method
This recipe produces pairwise alignments with different algorithms.
This recipe demonstrates variant calling using freebayes on simulated data.
This recipe demonstrates variant calling using freebayes and simulated data.
This recipe aligns simulated reads with a short read aligner.
This recipe demonstrates the effects that large scale genomic variations have on the alignments.
This recipe performs an RNA Seq analysis of control samples using an alignment based method
This recipe demonstrates variant call generation using bcftools and simulated data.
This recipe performs an RNA Seq analysis of spiked control samples using an alignment based method
This recipe generates a heatmap for differential expression data
This recipe evaluates SNP callers on a the syndip data.
This recipe performs an RNA Seq analysis of control samples using a classification based method.
Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in …
This recipe can be a starting point for other recipes.
This recipe demonstrates the use of makefiles.
This recipe prints the bash environment used to run the script.
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