Update README.md

Author: alexandrutomescu

README.md

@@ -16,17 +16,17 @@ To compile, run these:
 
 Quickstart: `./bin/GraphChainer -t 4 -f reads.fastq -g graph.gfa -a out.gam`
 
-Parameters inherited from GraphAligner:
-- `-t` Number of threads.
+Key parameters:
+- `-t` Number of threads (optional, default 1).
 - `-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. **This graph must be acyclic**. Format .gfa / .vg. 
 - `-a` Output file name. Format .gam or .json.
 
 Parameters related to colinear chaining:
-- `--speed <int>` Default 1. Use 2 or 3 (or larger values) if you want GraphChainer to be faster, but sligthly less accurate.
-- `--colinear-split-len <int>` Default 35. The length of the fragments in which the long read is split to create anchors.
-- `--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 <int>` 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.
+- `--speed <int>` Use 2 or 3 (or larger values) if you want GraphChainer to be faster, but sligthly less accurate (default 1).
+- `--colinear-split-len <int>` The length of the fragments in which the long read is split to create anchors (default 35).
+- `--colinear-split-gap <int>` The distance between consecutive fragments (default 35). If `--speed` is set, then always `--colinear-split-gap = --speed * --colinear-split-len`.
+- `--colinear-gap <int>` When converting an optimal chain of anchors into an alignment path, split the path if the distance in the graph between consecutive anchors is greater than this value (default 10000).
 
 ### Constructing an (acyclic) variation graph