From 1916d486376b250125ca2c66c3e69cb2dd0381fb Mon Sep 17 00:00:00 2001 From: JianJun Jin Date: Fri, 12 Apr 2024 18:55:06 -0400 Subject: [PATCH 1/2] Update brief usage --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 17c0ca1..6f27293 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,15 @@ pip install ./Traversome --no-deps ### Command line interface (CLI) ```bash -traversome thorough -g graph.gfa -a align.gaf -o outdir --topo circular --chr all +traversome thorough -g graph.gfa -a align.gaf -o outdir --topo circular --v-comp all +``` + +Important optional flags to finetune for achieving valid result (high bootstrap support): + +``` +--min-align-id Threshold for alignment identity, below which the alignment will be discarded. [default: 0.992] +--min-align-len Threshold for alignment length, below which the alignment will be discarded. [default: 5000] +--min-align-counts Threshold for counts per path, below which the alignment(s) of that path will be discarded. [default: auto] ``` ### Interpreting results From 6dbce126879506aea6daa1ad578bdbe03566900c Mon Sep 17 00:00:00 2001 From: JianJun Jin Date: Fri, 12 Apr 2024 18:56:34 -0400 Subject: [PATCH 2/2] Update usage --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 6f27293..690e338 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,8 @@ Important optional flags to finetune for achieving valid result (high bootstrap --min-align-counts Threshold for counts per path, below which the alignment(s) of that path will be discarded. [default: auto] ``` +Use `traversome thorough -h` to see details for above flags and other flags. + ### Interpreting results ``` |-- output_dir