From d3906b3bb971428ba9c9ec7003286a68d88a7cc8 Mon Sep 17 00:00:00 2001
From: Johannes Debler <johannes.debler@gmail.com>
Date: Thu, 6 Feb 2025 15:49:16 +1000
Subject: [PATCH] Update README.md

dorado correct doesn't generate FASTQ files, so these two lines need to be changed to FASTA
---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 8b1f808b..b2cb4adf 100644
--- a/README.md
+++ b/README.md
@@ -500,10 +500,10 @@ dorado basecaller <model> pod5s/ --emit-moves > calls.bam
 samtools fastq calls.bam > calls.fastq
 
 # Apply dorado correct to a set of reads that can be used as input in an assembly program.
-dorado correct calls.fastq > corrected.fastq
+dorado correct calls.fastq > corrected.fasta
 
 # Assemble the genome using those corrected reads
-<some_assembler> --input corrected.fastq > draft_assembly.fasta
+<some_assembler> --input corrected.fasta > draft_assembly.fasta
 
 # Align original calls to the draft assembly
 dorado aligner calls.bam draft_assembly.fasta > aligned_calls.bam