diff README.txt @ 24:c8f88ae512f3 draft default tip

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+PROGRAM
+=======
+
+PhageTerm.py - run as command line in a shell
+
+
+UPDATES
+=======
+
+Bug fix:
+When the repeat region (of DTR phages) wraps around the reference contig ends, the first and last bases of the repeat region were missing in the reported sequence.
+Bug fixed thanks to Matthew Lueder (Naval Medical Research Center-Frederick).
+
+Bug fix: cohesive sequence of COS 3' phages are now correctly determined. 
+Thanks to Dr Wei Shen.
+
+VERSION
+=======
+
+Version 1.0.12
+
+
+INTRODUCTION
+============
+
+PhageTerm software is a tool to determine phage termini and packaging mode
+from high throughput sequences that rely on the random fragmentation of DNA (e.g. 
+Illumina TruSeq). Phage sequencing reads from a fastq file are aligned to the phage 
+reference genome in order to calculate two types of coverage values (whole genome coverage 
+and the starting position coverage). The starting position coverage is used to perform a 
+detailed termini analysis. If the user provides the host sequence, reads that does not 
+match the phage genome are tested on the host using the same mapping function.
+
+The PhageTerm program and information is available at https://sourceforge.net/projects/phageterm/
+
+A Galaxy wrapper version is also available at https://galaxy.pasteur.fr
+
+
+PREREQUISITES
+=============
+
+Unix/Linux
+
+- Python      	2.7
+- matplotlib  	2.0.2
+- numpy       	1.11
+- pandas      	0.19.1
+- scikit-learn	0.18.1
+- scipy       	0.19.0
+- statsmodels 	0.8.0
+- reportlab   	3.4.0
+
+
+COMMAND LINE
+============
+
+
+	./PhageTerm.py -f reads.fastq -r phage_sequence.fasta [-n phage_name -p reads_paired 
+	-s seed_lenght -d surrounding -t installation_test -c nbr_core -g host.fasta 
+	(warning increase process time)]
+
+    
+	Help:   
+    
+        ./PhageTerm.py -h
+        ./PhageTerm.py --help
+    
+    Options:
+
+	Raw reads file in fastq format:
+    -f INPUT_FILE, --fastq=INPUT_FILE
+                        Fastq reads 
+                        (NGS sequences from random fragmentation DNA only, 
+                        e.g. Illumina TruSeq)
+                        
+	Raw reads file in fastq format:
+    -p INPUT_FILE, --paired=INPUT_FILE
+                        Paired fastq reads 
+                        (NGS sequences from random fragmentation DNA only, 
+                        e.g. Illumina TruSeq)                       
+                        
+	Phage genome in fasta format:
+    -r INPUT_FILE, --ref=INPUT_FILE
+                        Reference phage genome as unique contig in fasta format
+
+	Name of the phage being analyzed by the user:
+    -n PHAGE_NAME, --phagename=PHAGE_NAME
+                        Manually enter the name of the phage being analyzed.
+                        Used as prefix for output files.
+
+	Lenght of the seed used for reads in the mapping process:
+    -s SEED_LENGHT, --seed=SEED_LENGHT
+                        Manually enter the lenght of the seed used for reads
+                        in the mapping process (Default: 20).
+
+	Lenght of the seed used for reads in the mapping process:
+    -d SUROUNDING_LENGHT, --surrounding=SUROUNDING_LENGHT
+                        Manually enter the lenght of the surrounding used to
+                        merge close peaks in the analysis process (Default: 20).
+
+	Host genome in fasta format:
+    -g INPUT_FILE, --host=INPUT_FILE
+                        Reference host genome as unique contig in fasta format
+                        Warning: increase drastically process time
+
+	Core processor number to use:
+    -c CORE_NBR, --core=CORE_NBR
+                        Number of core processor to use (Default: 1).
+                        
+	Define phage mean coverage:
+    -m MEAN_NBR, --mean=MEAN_NBR
+                        Phage mean coverage to use (Default: 250).                        
+                                       
+	Software run test:
+    -t TEST_VALUE, --test=TEST_VALUE
+                        TEST_VALUE=C5   : Test run for a 5' cohesive end (e.g. Lambda)                        
+               			TEST_VALUE=C3   : Test run for a 3' cohesive end (e.g. HK97)
+               			TEST_VALUE=DS   : Test run for a short Direct Terminal Repeats end (e.g. T7)
+               			TEST_VALUE=DL   : Test run for a long Direct Terminal Repeats end (e.g. T5)
+               			TEST_VALUE=H    : Test run for a Headful packaging (e.g. P1)
+               			TEST_VALUE=M    : Test run for a Mu-like packaging (e.g. Mu)
+               
+                        
+OUTPUT FILES
+==========
+
+	(i) Report (.pdf)
+	
+	(ii) Statistical table (.csv) 
+
+	(iii) Sequence files (.fasta)
+	
+
+CONTACT
+=======
+
+Julian Garneau <[e-mail]>
+Marc Monot <[e-mail]>
+David Bikard <[e-mail]>