diff --git a/README.md b/README.md index ad728ce..a177c3e 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ conda install groot ### Source -`GROOT` is written in Go (v1.9) - to compile from source you will first need the [Go tool chain](https://golang.org/doc/install). Once you have it, try something like this to compile: +`GROOT` is written in Go (v1.10) - to compile from source you will first need the [Go tool chain](https://golang.org/doc/install). Once you have it, try something like this to compile: ```bash # Clone this repository @@ -73,7 +73,15 @@ groot index -i arg-annot.90 -o groot-index -l 100 # Align reads and report groot align -i groot-index -f reads.fq | groot report ``` ->note: you must run the index subcommand using your query read length (e.g. `-l 100` for 100bp reads) +>note: index the graph using a window size <= your maximum expected read length, so for 100bp reads, use `-l 100` + +If you anticipate variable read lengths, index the graphs for containment searching: + +```bash +# Create graphs and index for containment searching +groot index -i arg-annot.90 -o groot-index -l 100 --containment -j 0.5 +``` +>note: the above command will allow you to align reads of any length (up to `-l 100`) to the graphs, within a containment threshold of 0.5 (`-j 0.5`) ## Further Information & Citing diff --git a/src/version/version.go b/src/version/version.go index 12900c6..a0ec1b2 100644 --- a/src/version/version.go +++ b/src/version/version.go @@ -1,3 +1,3 @@ package version -const VERSION = "0.8.0" +const VERSION = "0.8.1"