From 64620bd07b556a316a5808af3f2222bcf88a8e51 Mon Sep 17 00:00:00 2001 From: christopher-hakkaart Date: Thu, 24 Mar 2022 19:18:46 +0100 Subject: [PATCH] Update readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a2676407..726eeff3 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,8 @@ On release, automated continuous integration tests run the pipeline on a [full-s * Convert SAM to co-ordinate sorted BAM and obtain mapping metrics ([`SAMtools`](http://www.htslib.org/doc/samtools.html)) 6. Create bigWig ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/)) and bigBed ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedToBigBed`](http://hgdownload.soe.ucsc.edu/admin/exe/)) coverage tracks for visualisation 7. DNA-specific downstream analysis: - * DNA variant calling ([`medaka`](https://github.com/nanoporetech/medaka) and/or [`sniffles`](https://github.com/fritzsedlazeck/Sniffles)) + * DNA short variant calling ([`medaka`](https://github.com/nanoporetech/medaka)) + * DNA structural variant calling ([`sniffles`](https://github.com/fritzsedlazeck/Sniffles)) 8. RNA-specific downstream analysis: * Transcript reconstruction and quantification ([`bambu`](https://bioconductor.org/packages/release/bioc/html/bambu.html) or [`StringTie2`](https://ccb.jhu.edu/software/stringtie/)) * bambu performs both transcript reconstruction and quantification.