From 918b07146e7583c518b49c83568c4efb5cc44070 Mon Sep 17 00:00:00 2001 From: Li Song Date: Sat, 28 Dec 2024 01:38:20 -0500 Subject: [PATCH] Create README.md for script folder --- scripts/README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 scripts/README.md diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 0000000..fbf6887 --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,11 @@ +## taxonomy.py +A python script to obtain various information from the nodes.dmp file downloaded from NBCI. Run "python3 taxonomy.py -h" for more information + +## requant-centrifuge.pl +The perl script that can use centrifuger-quant to recalculate the abundance from Centrifuge classification result. +It takes four parameters, in the order of: path to Centrifuge, path to Centrifuger, Centrifuge's index prefix, Centrifuge's classification output. +An example is: +``` + perl requant-centrifuge.pl ./centrifuge/ ./centrifuger/ cf_idx/p_compressed+h+v cf_classification.out > new_report.tsv +``` +The idea of the script is to run "centrifuge-inspect" to get the taxonomy tree, name, and genome size from Centrifuge's index, and then run "centrifuger-quant" to get the report.