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                                Next Generation Sequencing Short Read Trimmer (ngsShoRT)

Sari Khaleel (Sari.S.Khaleel.DM AT dartmouth.edu)
Dartmouth Medical School
Last updated 01-13-2014
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NOTE: ngsShoRT.pl and its modules require the following CPAN modules to be installed in your perl library:

                              Log in as root, then
                               $ perl -MCPAN -e shell
                               cpan> install String::Approx
                               cpan> install PerlIO::gzip
                               
                              See http://www.cpan.org/modules/INSTALL.html for more info on installing the module 
                              If you have problems installing this module, See startup_tutorial.pdf to get around it
- warnings
- strict
- Getopt::Long


The following directory contains:

1. ngsShoRT.pl
--------------
The interface script of ngsShoRT.

For usage, $ perl ngsShoRT.pl   OR    $ perl ngsShoRT.pl --help
For detailed usage, see See manuals/quick_manual.txt (4)

The script takes all its parameters from commandline input or from a text input file (a modified copy of 
input_file_TEMPLATE.txt, see 3). See manuals (4) for more detail.


2. Manual_2.1.pdf (START HERE)
-------------------------------------
A printer-friendly tutorial to get you started with ngsShoRT.pl


3. five_prime_adapter_seq_template.txt
-----------------------------------
A template file for 5' adaptor/primer sequences, which are used by the five_prime_PE_adapter_trim.pm module to trim 
out these sequences from both PE reads. See manual for more details.
  The file contains a list of sequences along with the number of bases before and after the detected adaptor/primer 
sequence that the user may want to be trimmed out as well.


4. illumina_and_454_primers (directory)
----------------------------------------
Contains primer libraries for Illumina and 454 that can be used to trim with 5adpt using the -5a_f option and their
appropriate code:
- Available Illumina libraries are:  i-g (Illumina genomic, Default), i-p (Illumina PE), i-m (Illumina multiplex), 
								     i-n (Illumina NlaIII), i-d (Illumina DpnII), i-r (Illumina sRNA)

- Available 454 (pyrosequencing) libraries are: p-b (pyroseq basic), p-r (pyroseq sRNA), p-p (pyroseq PE), 
                                                p-a (pyroseq amplicon)

5. sample_data  (directory)
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Contains the first 2000 Fastq PE and Single read pairs from SRR065390 (Caenorhabditis elegans whole genome study).
There are also single qseq reads. More details on how I got these sequences can be found at sample_data/README.txt 


6. modules_and_objects (directory)
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Contains the read and PE pair classes, trimming modules, report modules, processing modules. Under-the hood Module 
and class structure of ngsShoRT is explained in the manual (6).


7. misc_scripts
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These are supporting scripts that we used frequently with our assembly projects
 
 a. assembly_summary_1.0
 -----------------------
   Essentially, assembly_summary is a script that takes an assembled contigs file and returns its contiguity statistics
   (total length, meand and median contig length, N25 - N90, GC content, etc). However, this script is modified for big
   assembly projects where there are many assemblies (different datasets, different K-values for the Velvet/SOAP/etc 
   assembly) located at different directories. 
   
   It's also capable of creating csv-formatted single-stat tables that can be readily loaded to excel to create assembly
   charts. See the assembly_summary/chart_tutorial.pdf for more info.
   
   
