From d858e1b6b9396087ad3ed5261eb4e50ca8ceac80 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-Fran=C3=A7ois=20Flot?= Date: Mon, 20 Jul 2020 02:14:14 +0200 Subject: [PATCH 1/3] Update README.md --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 11d0259..26eba56 100644 --- a/README.md +++ b/README.md @@ -7,10 +7,10 @@ # BCOOL de Bruijn graph cOrrectiOn from graph aLignment -## Dependancies -Bcool clone and compile Bcalm2 Bgreat2 Btrim and Ntcard +## Dependencies +The installation script of Bcool compiles Bcalm2, Bgreat2, Btrim and ntCard. -It require GCC>=4.9.1, CMAKE>=3.3 and Python 3 +This requires GCC>=4.9.1, CMAKE>=3.10, Autoconf, Automake and Python 3. ## Installation @@ -28,7 +28,7 @@ For a faster install using 8 cores `./test.sh` -Bcool will be tested with a fixed kmer size and with ntcard +Bcool will be tested with a fixed kmer size and with ntCard It should output @@ -38,7 +38,7 @@ and `IT WORKS with ntcard!` -If only the first message is present, you can still use Bcool but you need to give a size of k to perform correction +If only the first message is present, you can still use Bcool but you need to give a size of k to perform correction. From c9c61784f2d94ae253509521a247950a80e08a0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-Fran=C3=A7ois=20Flot?= Date: Mon, 20 Jul 2020 02:21:18 +0200 Subject: [PATCH 2/3] Update README.md --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 26eba56..9d20dbe 100644 --- a/README.md +++ b/README.md @@ -7,8 +7,11 @@ # BCOOL de Bruijn graph cOrrectiOn from graph aLignment +[Limasset A, Flot J-F, Peterlongo P (2020) Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 36:1374–1381](https://doi.org/10.1093/bioinformatics/btz102) + + ## Dependencies -The installation script of Bcool compiles Bcalm2, Bgreat2, Btrim and ntCard. +The installation script of Bcool compiles [Bcalm2](https://github.com/GATB/bcalm), [Bgreat2](https://github.com/Malfoy/BGREAT2), [Btrim](https://github.com/Malfoy/BTRIM) and [ntCard](https://github.com/bcgsc/ntCard). This requires GCC>=4.9.1, CMAKE>=3.10, Autoconf, Automake and Python 3. From 6605e2eec17aa0d160f2ce78819c2ffe3f44eb2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jean-Fran=C3=A7ois=20Flot?= Date: Mon, 20 Jul 2020 02:45:39 +0200 Subject: [PATCH 3/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9d20dbe..f5414f6 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Build Status](https://travis-ci.org/Malfoy/BWISE.svg?branch=master)](https://travis-ci.org/Malfoy/BCOOL) -# BCOOL +# Bcool de Bruijn graph cOrrectiOn from graph aLignment [Limasset A, Flot J-F, Peterlongo P (2020) Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 36:1374–1381](https://doi.org/10.1093/bioinformatics/btz102)