From cbc319e62049f381c296f31d559a0c21f651b84f Mon Sep 17 00:00:00 2001 From: Ksenia Date: Fri, 6 Sep 2024 13:14:37 +0100 Subject: [PATCH] Update output.md --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index f753555..fedc59b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -7,7 +7,7 @@ This document describes the output produced by the genomeassembly pipeline. The standard assembly pipeline contains running hifiasm on the HiFi reads, purging the primary contigs with purge_dups, and scaffolding them up with YaHS. Optionally, if Illumina 10X data is provided, the purged contigs and haplotigs can be polished. -In case of a diploid genome when HiFi and HiC data is coming from the same individual addtionally hifiasm can be run in HiC mode to produce a phased assembly. In that case the produced haplotypes are not purged but scaffolded up directly with YaHS. +In case of a diploid genome when HiFi and HiC data come from the same individual an additional hifiasm run in HiC mode produces two balanced fully phased haplotypes. The haplotypes are not purged but scaffolded up directly with YaHS. Optionally, the organelles assembly can be triggered. The mitochondrion and (if relevant) plastid sequences are produced using MitoHiFi and OATK.