From c44357926f79fa3aca409779d13aa9f957989442 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 14 Oct 2014 23:46:59 -0400 Subject: [PATCH] updated README, a bit --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3472e91..250a009 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,6 @@ do not have plan to submit it to a peer-reviewed journal in the near future. 3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb) 4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0) 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref) -6. [How to map sequences to GRCh38 with ALT contigs?](#h38) ####1. What types of data does BWA work with? @@ -93,6 +92,10 @@ settings: bwa mem -x pacbio ref.fa reads.fq > aln.sam +* Oxford Nanopore reads to a reference genome: + + bwa mem -x ont2d ref.fa reads.fq > aln.sam + BWA-MEM is recommended for query sequences longer than ~70bp for a variety of error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small.