Sameer

Program to get mapping statistics, generate consensus and to get low frequency variats from a sam file.

Installation

git clone https://github.com/vbsreenu/Sameer.git
cd Sameer
cc sameer_new.c -o SAMEER_NEW
chmod +x SameerReport
chmod +x *.R 

** Set the path to the installation directory to access these programs. (This is dependent on your shell) **

Usage

SameerReport input.sam annotation.tsv Ref.fa

Demo run

cd demo
unzip 1-MRU25010-M-mapped.sam.zip
cd ..
./SameerReport demo/1-MRU25010-M-mapped.sam demo/MRU25010-M.anno demo/MRU25010-M.fa

Here 1st input is a SAM file 2nd input is an annotation file. This is a tab seperated file with four columns, ORF start, ORF end, ORF orientation and Name. 3rd input is the reference file used for mapping

Output

This will produce a PDF file with the detailed summary and text file of amino acid variations (variations.txt). In the demo output it should look like...

Glycoprotein    21-3614 1198
1 M M   M: 99.66(583)
2 Y Y   Y: 99.37(634)
3 V V   V: 100.00(1120)
4 L L   L: 99.93(1399)
5 L L   L: 99.93(1422)
6 T T   T: 100.00(1498)
7 I I   I: 99.93(1530)
8 L L   L: 99.94(1687)
9 I I   I: 99.88(1724)
10 S S  S: 99.89(1895)

PDF output (1-MRU25010-M-mapped.pdf) can be see in demo direcory.

Dependencies:

• Latex
• R
• gcc (or cc)