========================================================== deML: Maximum likelihood demultiplexing for NGS data

QUESTIONS : gabriel [dot] reno [ at sign ] gmail.com

About

deML is a program for maximum likelihood demultiplexing

Downloading:

Go to https://github.com/grenaud/deML and either:

1. Download ZIP

or

2. Do a "git clone --recursive https://github.com/grenaud/deML.git"

Installation:

1. Build Bamtools first:

   cd bamtools/
   mkdir build/
   cd build/ cmake .. make cd ../..

2. Build the submodules and main code by typing :

   make

running the program:

To launch the program simply type:

src/deML

Test data:

For raw BAM files:

src/deML -i testData/index.txt -o testData/demultiplexed.bam testData/todemultiplex.bam

For FASTQ files

src/deML -i testData/index.txt -f testData/todemultiplex.fq1.gz  -r testData/todemultiplex.fq2.gz -if1 testData/todemultiplex.i1.gz  -if2 testData/todemultiplex.i2.gz  -o testData/demultiplex

-o testData/demultiplexed.bam testData/todemultiplex.bam

Format for input

You can either specify the actual sequences used for multiplexing:

#Index1 Index2 Name AATTCAA CATCCGG RG1 CGCGCAG TCATGGT RG2 AAGGTCT AGAACCG RG3 ACTGGAC TGGAATA RG4 AGCAGGT CAGGAGG RG5 GTACCGG AATACCT RG6 GGTCAAG CGAATGC RG7 AATGATG TTCGCAA RG8 AGTCAGA AATTCAA RG9

or you can also specify the raw indices:

#Index1 Index2 Name 341 33 RG1 342 34 RG2 343 35 RG3 344 36 RG4 345 37 RG5 346 38 RG6 347 39 RG7 348 40 RG8 349 41 RG9