From 4e7a091f93237fb7179997e5909f3760548b4cf3 Mon Sep 17 00:00:00 2001 From: JianJun Jin Date: Tue, 7 Jan 2025 22:10:52 +0800 Subject: [PATCH] Update usage 0.1.7.1 --- README.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 690e338..60cafb6 100644 --- a/README.md +++ b/README.md @@ -30,15 +30,16 @@ pip install ./Traversome --no-deps ### Command line interface (CLI) ```bash -traversome thorough -g graph.gfa -a align.gaf -o outdir --topo circular --v-comp all +traversome thorough -g graph.gfa -a align.gaf -o outdir --topo circular ``` 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] +--min-read-id Threshold for alignment identity, read with below which the alignment will be discarded. [default: 0.992] +--min-record-id Threshold for alignment identity, a record of a read with below which the alignment will be discarded. [default: 0.99] +--min-align-len Threshold for the continuous alignment length of a read, 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. The default automatic selection (-1) does not guarantee the best performance - good bootstrap support. [default: auto] ``` Use `traversome thorough -h` to see details for above flags and other flags. @@ -50,5 +51,9 @@ Use `traversome thorough -h` to see details for above flags and other flags. |-- variants.info.tab information of survival variants after model selection and bootstrap |-- bootstrap.replicates.tab bootstrap results |-- final.result.tab summary of pangenome solutions + |-- variant.*.fasta sequence of each variant in the best supported result |-- pangenome.gfa pangenome graph of the best supported result + |-- options.yaml information of options + |-- readpath.information.tab read path index -> alignment record indices + |-- readpath.record_ids.tab information of read paths and their congruent variant ```