Create README.md

Author: govinda-kamath

README.md

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+# AwesomeAssembler
+
+CI Status: 
+
+master:![image](https://travis-ci.com/fxia22/HINGE.svg?token=i41xfGcHb72GYFyZnvtg&branch=master)
+
+dev:![image](https://travis-ci.com/fxia22/HINGE.svg?token=i41xfGcHb72GYFyZnvtg&branch=dev)
+
+## Introduction 
+
+AwesomeAssembler is an experimental long read assembler based on an idea called _hinging_. Now AwesomeAssembler is at research prototype stage.
+
+## Pipeline Overview
+
+AwesomeAssembler is an OLC(Overlap-Layout-Consensus) assembler. The idea of the pipeline is shown below. 
+
+![image](High_level_overview.png)
+
+At a high level, the algorithm can be thought of a variation of the classical greedy algorithm.
+The main difference with the greedy algorithm is that rather than each read having a single successor,
+and a single predecessor, we allow a small subset of reads to have a higher number of successors/predecessors.
+This subset is identified by a process called _hinging_. This helps us to recover the graph structure
+directly during assembly.
+
+Another significant difference from HGAP or Falcon pipeline is that it does not have a pre-assembly or read correction step. 
+
+
+
+## Algorithm Details
+
+### Reads filtering
+Reads filtering filters reads that have long chimer in the middle, and short reads.
+Reads which can have higher number of predecessors/successors are also identified there. 
+This is implemented in `filter/filter.cpp`
+
+### Layout 
+The layout is implemented in `layout/hinging.cpp`. It is done by a variant of the greedy algorithm.
+
+The graph output by the layout stage  is post-processed by running `scripts/pruning_and_clipping.py`.
+One output is a graphml file which is the graph representation of the backbone.
+This removes dead ends and Z-structures from the graph enabling easy condensation.
+It can be analyzed and visualized, etc. 
+
+
+## Parameters
+
+In the pipeline described above, most programs not only takes the input file and output file as arguments, but also require a configuration file in ini format. This consists parameters for each step in the pipeline, and their usage and effects are explained below:
+
+
+###[filter]
+- length_threshold = 6500; // Length threshold for reads to be considered in the backbone
+- quality_threshold = 0.23; // Quality threshold for edges to be considered in the backbone 
+- n_iter = 2; // iterations of filtering, the filtering needs several iterations, because when filter reads, you got rid of some edges; when filter edges, you got rid of some reads (if the last edge is filtered.) Typically 2-3 iterations will be enough.
+- aln_threshold = 2500; // Length of alignment for edges to be considered in the backbone
+- min_cov = 5; // Minimal coverage for a segment to be considered not chimer/adaptor
+- cut_off = 200; // A parameter for identifying long chimer in the middle of a read
+- theta = 300; // A parameter for tolerance of the overhang length when looking for right extension.
+
+
+###[running]
+- n_proc = 12; // number of CPUs for layout step
+
+###[draft]
+- min_cov = 10; //obsolete
+- trim = 200; //obsolete
+- edge_safe = 100; //obsolete
+- tspace = 900; //space between new "trace points"
+
+
+###[consensus]
+- min_length = 2000; // Minimal length of reads used for final consensus
+- trim_end = 200; // Trim ends for alignments for final consensus
+- best_n = 1; // If one read has multiple alignments with the bacbone assembly, choose the longest n segments for consensus.
+- quality_threshold = 0.23; // alignment quality threshold
+
+# Installation
+
+This software is still at prototype stage so it is not well packaged, however it is designed in a modular flavor so different combinations of methods can be tested. 
+
+Installing the software is very easy. 
+
+```
+git clone https://github.com/Eureka22/AwesomeAssembler.git
+git submodule init
+git submodule update
+./build.sh
+```
+
+# Running
+
+In order to call the programs from anywhere, I suggest one export the directory of binary file to system environment, you can do that by using the script `setup.sh`.
+
+A demo run for assembling the ecoli genome is the following:
+
+```
+source setup.sh
+mkdir data/ecoli
+cd data/ecoli
+# reads.fasta should be in data/ecoli
+fasta2DB ecoli reads.fasta
+DBsplit -x500 -s100 ecoli     
+HPCdaligner -t5 ecoli | csh -v
+# alternatively, you can put output of HPCdaligner to a bash file and edit it to support 
+rm ecoli.*.ecoli.*
+LAmerge ecoli.las ecoli.*.las
+rm ecoli.*.las # we only need ecoli.las
+DASqv -c100 ecoli ecoli.las
+
+# Run filter
+Reads_filter --db ecoli --las ecoli.las -x ecoli --config /utils/nominal.ini
+
+# Run layout
+hinging --db ecoli --las ecoli.las -x ecoli --config /utils/nominal.ini -o ecoli
+
+# Run postprocessing
+
+python pruning_and_clipping.py ecoli.edges.hinges ecoli.hinge.list <identifier-of-run>
+```
+
+## Debugging
+
+### showing ground truth on graph
+Some programs are for debugging and oberservation. For example, one can get the ground truth by mapping reads to reference and get `ecoli.ecoli.ref.las`.
+
+This `las` file can be parsed to json file for other programs to use. 
+
+```
+run_mapping.py ecoli ecoli.ref ecoli.ecoli.ref.las 1-$ 
+```
+
+In the prune step, if `ecoli.mapping.json` exists, the output `graphml` file will contain the information of ground truth. 
+
+### drawing alignment graphs and mapping graphs
+Draw a read, for example 60947, and output figure to `sample` folder (need plus 1 as LAshow counts from 1):
+
+```
+draw2.py ecoli ecoli.las 60948 sample 100
+```
+
+Draw pileup on draft assembly, given a region(start,end):
+
+```
+draw2_pileup_region.py  3600000 4500000 
+```
+
+# Results:
+
+For ecoli 160X dataset,  after shortening reads to have a mean length of 3500 (with a variance of 1500), the graph is preserved.
+
+![image](ecoli_shortened.png)
+
+The graph returned by Falcon here is
+
+![image](Falcon_ecoli_shortened.png)