# Installation

How to install the wrapper scripts:

    # Create a folder for scripts.
    mkdir -p ~/bin

    # Install the wrappers for the EMBOSS aligners.
    curl http://data.biostarhandbook.com/align/global-align.sh > ~/bin/global-align.sh
    curl http://data.biostarhandbook.com/align/local-align.sh > ~/bin/local-align.sh

    # Make the scripts executable.
    chmod +x ~/bin/*-align.sh

# global-align.sh

Usage:

    global-align.sh THISLINE ISALIGNED

or on files:

	global-align.sh file1.fa file2.fa

in both cases you may pass additional parameters like:

	global-align.sh THISLINE ISALIGNED -gapopen 9 -gapextend 5

Tip: Replace the tool `needle` with the tool named `stretcher`
for a less rigorous but better performing algorithm.

# local-align.sh

Usage:

    local-align.sh THISLINE ISALIGNED

or on files:

	local-align.sh file1.fa file2.fa

Tip: Replace the tool `water` with the tool named `matcher`
for a less rigorous but better performing algorithm.

# perfect_coverage.py

Generates perfect coverage data:

	# Get the script
	curl -O http://data.biostarhandbook.com/align/perfect_coverage.py

	# Usage:
	cat  genome.fa | python perfect_coverage.py

Produces the files `R1.fq` and `R2.fq`

# bowtie2-parameter-sweep.sh

Sweeps through the bowtie2 parameters space and attempts
to evaluate the parameters' effect on alignment rates.

Outputs the number of concordant, discordant and one time alignments.

Based on a script by Fan Song submitted for an assignment. Fan Song writes:

>The parameters that I think will influence the results the most
> are -D, -R, -N, -L, and -i."

The range for these parameters are

* `D: [5, 15]`, give up extending after <int> failed extends in a row (15)
* `R: [1, 3]`, for reads w/ repetitive seeds, try <int> sets of seeds (2)
* `N: [0, 1]`, max number of mismatches in seed alignment; can be 0 or 1 (0)
* `L: [15, 25]`, length of seed substrings; must be >3, <32 (22)
* `i1: [0, 1]`, interval between seed substrings w/r/t read len (S,1,1.15)
* `i2: [0.5, 2.5]` with a increment of 0.25

for a total of `10365`` combinations:

Get the script

	curl -O http://data.biostarhandbook.com/align/bowtie2-parameter-sweep.sh

Usage:

	bash bowtie2-parameter-sweep.sh

or to set an error rate of `10%`:

	bash bowtie2-parameter-sweep.sh 0.1

# simulate-exprimental-data.sh

This script simulates a sequencing run from an accession number.

You cam mutate the genome genome by hand - or as it is in the script.
Then run this tool generate alignments and visualize these alignments in IGV.


A typical run will be:

    *** Obtain data for AF086833 and save it as refs/REFERENCE.fa.
    *** Index refs/REFERENCE.fa with several tools.
    *** Mutating refs/REFERENCE.fa to refs/GENOME.fa
    *** Generating simulated reads from: refs/GENOME.fa
    *** Aligning the reads into: results.bam