Bioinformatics Recipe Cookbook
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The recipe demonstrates the use of different short read aligners.

There substantially many more differences between aligners beyond their "performance" or so-called "accuracy". Equally important is how we can customize the alignments and what additional information is produced in each of the alignments.

The recipe generates SAM alignment files with different algorithms bwa, bowtie2 in both single end and paired-end mode.

  1. Downloads the 1976 Ebola - Mayinga Reference Genome
  2. Downloads paired-end sequencing data for the 2014 outbreak
  3. Generates single-end sequence alignments with bwa and bowtie2
  4. Generates paired-end sequence alignments with bwa and bowtie2
  5. Runs samtools flagstat on each of the SAM files.

Readers are invited to investiage the SAM files to identify the differences between aligner outputs.

Lecture

A detailed presentation that explains the steps and rationale for this recipe can be found at:

Please refer to the lecture above for study materials and additional content.

Recipe Code
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Integer values
                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
                    
Float values
                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
                    
Text box
                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
                    
Dropdown menu
                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
                    
Check box
                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
                    
Upload Field
                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
                    
Pick Data
                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
                    
Radio Buttons
                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
                    
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