From 04ec1fc5392e6f85985497b1da450a726b6ba077 Mon Sep 17 00:00:00 2001 From: Ryu Hyunwoo Date: Mon, 5 Feb 2024 17:37:03 +0900 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 19e971e..e243c66 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ GDBr : Genome identification tool for Double-strand Break Repair ================================================================ -`GDBr logo` GDBr (pronounced _Genome Debugger_) is tool that identify Double-strand Break Repair (DSBR) using genome and variant. GDBr goes through three processes to identify DSBR. First step is preprocess the genome using [`RagTag`](https://github.com/malonge/RagTag) and [`svim-asm`](https://github.com/eldariont/svim-asm) and make sure they have same chromosome name with reference. Second step is correcting the variant using [`BLAST`](https://blast.ncbi.nlm.nih.gov/Blast.cgi) and filtering the variant which have repeat bt [`TRF`](https://github.com/Benson-Genomics-Lab/TRF) and [`RepeatMasker`](https://github.com/rmhubley/RepeatMasker), then save a csv file. Last step is to segregate the corrected variants into the appropriate DSBRs. +GDBr logo GDBr (pronounced _Genome Debugger_) is tool that identify Double-strand Break Repair (DSBR) using genome and variant. GDBr goes through three processes to identify DSBR. First step is preprocess the genome using [`RagTag`](https://github.com/malonge/RagTag) and [`svim-asm`](https://github.com/eldariont/svim-asm) and make sure they have same chromosome name with reference. Second step is correcting the variant using [`BLAST`](https://blast.ncbi.nlm.nih.gov/Blast.cgi) and filtering the variant which have repeat bt [`TRF`](https://github.com/Benson-Genomics-Lab/TRF) and [`RepeatMasker`](https://github.com/rmhubley/RepeatMasker), then save a csv file. Last step is to segregate the corrected variants into the appropriate DSBRs. [![CI](https://github.com/Chemical118/GDBr/workflows/CI/badge.svg)](https://github.com/Chemical118/GDBr/actions?query=workflow%3ACI) [![codecov](https://codecov.io/gh/Chemical118/GDBr/branch/master/graph/badge.svg?token=NA5V5H52M6)](https://codecov.io/gh/Chemical118/GDBr) @@ -42,7 +42,7 @@ By using `RagTag` and `svim-asm`, `GDBr` preprocess data and return properly sca gdbr preprocess -r -q -o prepro -t ``` -The preprocess step requires the use of a sorting program to do the scaffolding and variant calling, and even though they are allocated a lot of threads, they still don't use them all. An optimization approach is to distribute multiple queries to a small number of threads. However, this approach requires very high memory usage, so GDBr was developed to allow the user to freely choose this optimization by providing the `--low_memory ` option. +The preprocess step requires the use of a sorting program to do the scaffolding and variant calling, and even though they are allocated a lot of threads, they still don't use them all. An optimization approach is to distribute multiple queries to a small number of threads. However, this approach requires very high memory usage, so GDBr was developed to allow the user to freely choose this optimization by providing the `--low_memory` option. #### Correct