From bd6fafb1716b43d2799c3f929006df15ed6db0b1 Mon Sep 17 00:00:00 2001 From: souvorov Date: Fri, 5 Oct 2018 16:45:25 -0400 Subject: [PATCH] Update README.md --- README.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 14ffa59..1640e2d 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,8 @@ For questions regarding SKESA, please contact Alexandre Souvorov (souvorov@ncbi.nlm.nih.gov) Richa Agarwala (agarwala@ncbi.nlm.nih.gov) -====================================================================== -I. COMPILATION +## Compilation Download current source code for SKESA $ git clone https://github.com/ncbi/SKESA @@ -32,9 +31,8 @@ I. COMPILATION These make files have been tested with BOOST v 1.62.0 and gcc v 4.9. -====================================================================== -II. SYNOPSIS +## Synopsis Running skesa @@ -102,9 +100,8 @@ II. SYNOPSIS Note that --sra_run option is not available if SKESA is built using Makefile.nongs -====================================================================== -II. SHORT DESCRIPTION +## Short description SKESA is a de-novo sequence read assembler for microbial genomes based on DeBruijn graphs. It uses conservative heuristics and is designed to @@ -160,9 +157,8 @@ II. SHORT DESCRIPTION reads but may give very small differences if read order is changed and insert size estimate is different. -====================================================================== -III. USAGE EXAMPLES +## Usage examples In all the examples below, we are providing 4 cores and have 48 Gb of memory. @@ -190,4 +186,9 @@ III. USAGE EXAMPLES $ skesa --sra_run SRR1695624 --sra_run SRR1745628 --cores 4 --memory 48 --use_paired_ends > SAMN03218571.skesa.fa -====================================================================== +## Citation + +Alexandre Souvorov, Richa Agarwala and David J. Lipman. +**SKESA: strategic k-mer extension for scrupulous assemblies.** +*Genome Biology* 2018 **19**:153. +[doi.org/10.1186/s13059-018-1540-z](https://doi.org/10.1186/s13059-018-1540-z)