CoSA

Coronavirus (SARS-Cov-2) sequencing analysis

Last Updated: 05.03.2021 (v9.0.0)

NOTE: This version of CoSA has only been tested with pbaa v0.1.3 and might not be compatible with pbaa versions above it

Stable version of CoSA under PacBio's GitHub

Developing version of CoSA under Magdoll's GitHub

Join the COVID19 Google Group to stay up-to-date on bioinfx recommendations and CoSA changes!

Updates

05.03.2021 v9.0.0 release. trim_MIPs.py added.

02.26.2021 v8.5.0 release. cleaned up unnecesary directories.

02.23.2021 v8.4.0 release. pbaa2vcf.py format update fix.

02.22.2021 v8.3.0 release. VCFCons.py now handles ill-formatted variants in CLC output.

02.21.2021 v8.2.0 release. pbaa2vcf.py now can handle edge cases of empty variants.

02.20.2021 v8.1.0 release. VCFCons.py can handle edge case of complete empty consensus and deals with unusual overlapping variant calls.

02.20.2021 v8.0.0 release. Added .vcfcons.variants.csv to VCFCOns.py output.

02.19.2021 v7.3.0 release. VCFCons.py accepts the new pbaa VCF type that follows standard AD info. Minor fixes to pbaa->VCF scripts.

02.17.2021 v6.1.0 release. Fixed VCFCons.py dealing with multiple ALT and proper INS if REF is more than 1nt.

02.15.2021 v6.0.0 release. Adding consensusVariants.py and pbaa2vcf.py for pbaa support.

02.14.2021 v5.2.0 release. VCFCons.py important bug fix on propagating deletions into consensus fasta.

02.11.2021 v4.0.0 release. VCFCons.py added.

What is CoSA

CoSA is a set of Python and R scripts for analyzing SARS-CoV-2 sequences from PacBio HiFi/CCS data.

Stable version Wiki

Developer version Wiki

How to install CoSA

To install, clone the repo and install:

$ git clone https://github.com/<ACCOUNT>/CoSA.git
$ cd CoSA
$ python setup.py build
$ python setup.py install