From b4f8cdbf96ba8c8dd37f4360b31ef9774d79d038 Mon Sep 17 00:00:00 2001
From: Xiaoli Dong <52679027+xiaoli-dong@users.noreply.github.com>
Date: Thu, 2 Nov 2023 10:59:49 -0600
Subject: [PATCH] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9a8fe61..769766a 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ By default, the pipeline supports both short and long reads:
     - Nanopore long read quality and length filter ([chopper](https://github.com/wdecoster/chopper))
     - Nanopore long read statistics ([seqkit stats](https://bioinf.shenwei.me/seqkit/usage/#stats))
 - Assembly
-  - Short read assembly with user choice of the assemblers ([Spades](https://github.com/ablab/spades) | [Skesa](https://github.com/ncbi/SKESA) | [Unicycler](https://github.com/rrwick/Unicycler) | [megahit](https://github.com/voutcn/megahit))
+  - Short read assembly with user choice of the assemblers ([Spades](https://github.com/ablab/spades) | [Skesa](https://github.com/ncbi/SKESA) | [Unicycler](https://github.com/rrwick/Unicycler) | [megahit](https://github.com/voutcn/megahit) | [shovill](https://github.com/tseemann/shovill)
   - Long read assembly is following the steps below:
     - Nanopore long read de novo assembly ([`Flye`](https://github.com/fenderglass/Flye))
     - Circular Flye contigs are rotated to start in the center of the contig ([in-house perl script](https://github.com/xiaoli-dong/pathogenseq/blob/main/bin/reset_start_position_for_circular_genome.pl))