covidPileup v1.1

Pipeline for COVID-19 variation analysis from whole genome sequences.

Download and Compile:

$ git clone  https://github.com/wtsi-hpag/covidPileup.git 
$ cd covidPileup 
$ bash install.sh

If everything compiled successfully you must see the final comment: "Congrats: installation successful!"

External packages

The genome aligner BWA (http://bio-bwa.sourceforge.net) and SMALT (http://www.sanger.ac.uk/science/tools/smalt-0) are downloaded and compiled by covidPileup.

Run the pipelines

Run covidPileup:

       $ /full/path/to/covidPileup/src/covidPileup -nodes <nodes> -SNP <plot> -GAP <plot> \
	 -country <country_name> -cover <n_cover> -length <reference_length> \
             reference.fasta COVID-19_genomes.fasta sample-pileup

       Parameters:
         nodes:        Number of CPUs requested  [ default = 30 ]
         length:       Reference genome length [ default = 40000 ]
         cover:        Threshold coverage number to report specific SNPs  [ default = 5 o] \
         country:      Specific SNPs in the country [ default = UK ]
                       "EU" and Europen countries like "France", "Italy" et al should work;
                       "UK" and "England", "Scotland", "Wales" et al should work;
         SNP:          Output 4 image files on SNP pileup [ default not plot ]
                       1. sample-pileup.pileupSNP.png; 2. sample-pileup.frequeSNP.png
                       3. sample-pileup.uniqueSNP.png; 4. sample-pileup.regionSNP.png

         GAP:          Output 2 image files on GAP pileup [ default not plot ]
                       5. sample-pileup.pileupGAP.png; 6. sample-pileup.frequeGAP.png

           Other output files:
         sample-pileup.name - country names and sample number for earch country
         sample-pileup.snps - all the SNPs detected by the pipeline
         sample-pileup.spec - country specific (unique) SNPs

Run example with reference.fasta COVID-19_genomes.fasta

       $ /full/path/to/covidPileup/src/covidPileup -nodes 30 -SNP plot -GAP plot -country UK\
	 reference.fasta COVID-19_genomes.fasta sample-pileup

or using SMALT $ /full/path/to/covidPileup/src/covidPileup -nodes 30 -SNP plot -GAP plot -country UK
-align smalt reference.fasta COVID-19_genomes.fasta sample-pileup

Data input fasta files

 The names in the fasta file have to follow the format used by Gisaid

 Australia/VIC110/2020
 USA/WA-UW-4032/2020
 England/20124095202/2020

Start a new run without doing the alignment

   The aligner SMALT is much slower than BWA, but it offers better alignments for sequences \
   (1) with a lot of "N"s; (2) lower sequence similarity such as bats or pangolins \
   Personally, I would recommend SMALT, which takes 2-3 hours with 60 CPUs for 50K genomes.

   If you had made a run previously with a temporary directory:       \ 

      /lustre/team117/zn1/project/covid/tmp_rununik_71885/            \

   You may use the already existing alignment file to save time:      \

       $ /full/path/to/covidPileup/src/covidPileup -nodes <nodes> -SNP <plot> -GAP <plot> \
	 -country <country_name> -cover <n_cover> -length <reference_length> \
             -data /lustre/team117/zn1/project/covid/tmp_rununik_71885/align.dat \
             reference.fasta COVID-19_genomes.fasta sample-pileup

   Note: "-data ?" expects a full path.