Update Manual

README.md

@@ -1,58 +1,17 @@
-Jabba: Hybrid Error Correction for Long Sequencing Reads using Maximal Exact Matches
+Jabba
 =====
 
-Jabba takes as input a concatenated de Bruijn graph and a set of sequences:
-- the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:  
-\>NODE	\<node number\>	\<size of node\>	\<number of in edges\>	\<in edges represented by node number of origin, separated by tabs\>	\<number of out edges\>	\<out edges represented by node number of target, separated by tabs\>  
-- the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba-\<input filename\>.fasta.
+Jabba, a hybrid error correction tool for sequencing reads.
 
-The output is a file with corrections of the long reads.
+To build Jabba run these commands in the `Jabba` folder:
 
+```bash
+> mkdir -p build
+> cd build
+> cmake ../
+> make
+```
 
-de Bruijn graph
-===============
-To build a de Bruijn graph from sequencing reads, one can use [brownie](https://github.com/jfostier/brownie), or any other suitable tool. Errors in the de Bruijn graph have to be corrected and linear paths concatenated. Correction can be achieved either by using corrected second generation data to build the graph or by directly correcting the graph.
 
-brownie will concatenate linear nodes and can output the graph in the desired graph format.  
-To build a graph with brownie from a fastq file short_reads.fastq containing short reads:  
->./brownie -p brownie_data -k 31 -g \<genome_size\> -fastq short_reads.fastq --graph  
-
-To build a graph with brownie from a fasta file genome.fasta containing a reference genome (in this case the graph is not corrected):  
->./brownie brownie_data -k 31 -fasta genome.fasta --perfectgraph  
-
-In both cases the graph file DBGraph.fasta will be produced.
-
-Installation
-============
-At the moment Jabba is available for Linux.
-Jabba can be compiled as follows:
->mkdir -p build  
->cd build  
->cmake ../  
->make
->cd ..  
->mkdir -p bin  
->cp -b ./build/src/Jabba ./bin/Jabba  
-
-Usage
-=====
->Jabba [options] [file_options] file1 [[file_options] file2]...  
-[options]  
-  -h	--help		display help page  
-  -i	--info		display information page  
- [options arg]  
-  -l	--length	minimal seed size [default = 20]  
-  -k	--dbgk		de Bruijn graph k-mer size  
-  -e	--essak		sparseness factor of the enhance suffix array [default = 1]  
-  -t	--threads	number of threads [default = available cores]  
-  -p	--passes	maximal number of passes per read [default = 2]  
- [file_options file_name]  
-  -o	--output	output directory [default = Jabba_output]  
-  -fastq		fastq input files  
-  -fasta		fasta input files  
-  -g	--graph		graph input file [default = DBGraph.txt]  
-
-examples:  
->./Jabba --dbgk 31 --graph DBGraph.txt -fastq reads.fastq  
-./Jabba -o Jabba -l 20 -k 31 -p 2 -e 12 -g DBGraph.txt -fastq reads.fastq  
+See the [Jabba manual](https://github.com/gmiclotte/Jabba/wiki) to get started.