The recipe generates simulated sequencing reads from NCBI accession numbers. It then performs class…
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 evaluates SNP callers on a the syndip data.
Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in …
The recipe attempts the find the most similar matches to a "mystery 16S sequence".
Use SAM flags to make scientific discoveries. (work in progress)
Perform data quality control on FASTQ data
RNA-Seq differential expression with alignments and using three different statistical methods.
Visualizing large scale genomic variations.
Half-sequence and half mythical-beast, "unaligned" BAM files are used to store FASTQ files.
The recipe demonstrates the use of different short read aligners.
The recipe demonstrates the effect of using different tasks may have on finding hits.
The recipe demonstrates the utility of blast databases for manipulating sequences.
A surprising number of analyses require that we compute genome or interval coverages.
Filtering Sequence Alignment Maps (SAM/BAM) files.
Bacterial variant caller
This recipe follows the variant calling process in the Biostar Handbook.
The recipe produces pairwise alignments with different software
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