sega

Self-orgnizing approach for metagenome

Installtion

cd src; make sega

Usage

Data Reprocessing

sega has a command seq2qu to transform the input sequences in FastA or FastQ format to their quanternary representation and concatenates them into a single sequence.

Examples:

bin/sega seq2qu test/ecoli_apec_o1.fasta test/ecoli_apec_o1.fasta.qu

Training

Models

See reference

Examples

If we want to know if there are two different codon usage patterns in E.coli, the option -c should be specified to be 2. We can run 10 iterations to see whether it converges. The training sequence is the first 50000*99 bps.

1. initilize phase labelling

    bin/sega train test/ecoli_apec_o1.fasta.qu tmp_dir -c 2 -k 10 n 50000 -w 99
   

2. initilize frequency tables

    bin/sega train test/ecoli_apec_o1.fasta.qu tmp_dir -p test/init_cut -c 2 -k 10 n 50000 -w 99