Merge branch 'master' of https://github.com/algbio/GraphChainer

Author: alexandrutomescu

README.md

@@ -1,6 +1,6 @@
 # GraphChainer
 
-Here we will version the main project consisting on building a sequence to graph aligner based on Co-linear Chaining.
+GraphChainer is an accurate aligner of long reads to a variation graph, based on co-linear chaining.
 
 #### Compilation
 
@@ -19,7 +19,7 @@ Quickstart: `./bin/GraphChainer -t 4 -f reads.fastq -g graph.gfa -a out.gam`
 Parameters inherited from GraphAligner:
 - `-t` Number of threads.
 - `-f` Input reads. Format .fasta / .fastq / .fasta.gz / .fastq.gz. You can input multiple files with `-f file1 -f file2 ...` or `-f file1 file2 ...`.
-- `-g` Input graph. Format .gfa / .vg.
+- `-g` Input graph. **This graph must be acyclic**. Format .gfa / .vg. 
 - `-a` Output file name. Format .gam or .json.
 
 Parameters related to colinear chaining:
@@ -28,6 +28,18 @@ Parameters related to colinear chaining:
 - `--colinear-split-gap <int>` Default 35. The distance between consecutive fragments. If `--speed` is set, then always `--colinear-split-gap = --speed * --colinear-split-len`.
 - `--colinear-gap 1000` Default 10000. When converting an optimal chain of anchors into an alignment path, split the path if the distance between consecutive anchors is greater than this value.
 
+### Constructing an (acyclic) variation graph
+
+Use [vg](https://github.com/vgteam/vg) and run:
+
+`vg construct -t 30 -a -r {ref} -v {vcf} -R 22 -p -m 3000000`
+
+### Citation
+
+If you use GraphChainer, please cite as:
+
+Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu. GraphChainer: Co-linear Chaining for Accurate Sequence-to-Variation-Graph Alignment. Submitted, 2021
+
 ### Credits
 
-GraphChainer is built on the excellent code base of [GraphAligner](https://github.com/maickrau/GraphAligner), which is released under [MIT License](https://github.com/maickrau/GraphAligner/blob/master/LICENSE.md). GraphAligner is described in the paper [GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment](GraphAligner: rapid and versatile sequence-to-graph alignment) by Mikko Rautiainen and Tobias Marschall.
+GraphChainer is built on the excellent code base of [GraphAligner](https://github.com/maickrau/GraphAligner), which is released under [MIT License](https://github.com/maickrau/GraphAligner/blob/master/LICENSE.md). GraphAligner is described in the paper [GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment](https://doi.org/10.1186/s13059-020-02157-2) by Mikko Rautiainen and Tobias Marschall.