#DENV_Phylo
##Introduction
DENV_Phylo is a bioinformtics pipeline that runs using nextfow. The pipeline is used to perform phylogenetic analysis of Dengue data from GISAID.
##Installation <<<<<<< HEAD Install docker as decribed here
clone the github repo:
git clone https://github.com/arnoldlambisia/DENV_Phylo.git
Install docker as decribed here
d6e9c83bd3dbbded98e5ec6f7f58903973006c9d
clone the github repo:
git clone https://github.com/arnoldlambisia/DENV_Phylo.git
##Pipeline The pipeline has four key processes:
- Data cleanup using (r-base)
This step uses an R script that takes inputs of a fasta and a metadata file downloaded from gisaid. The outputs are a renamed fasta file, subsampled accession IDs and fasta file and a metadata file for use with treetime.
- Alignment of subsampled fasta sequences using nextalign
The reference used is NC_001477 polyprotein for Dengue 1.
- Maximum likelihood tree genration using iqtree
parameters used: -m TEST -bb 1000 -T 4
- Creation of a time resolved tree using treetime
###Usage
The pipeline can be run suing the following command:
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docker run --rm -it -v <change directory to cloned repo>:$(pwd) alambisia/phylogen:1.0 nextflow run $(pwd)/main.nf --gisaid_fasta <insert fasta> --gisaid_metadata <insert metadata>
=======
docker run --rm -it -v \
<change directory to cloned repo>:$(pwd) alambisia/phylogen:1.0 nextflow run $(pwd)/main.nf \
--gisaid_fasta <insert fasta> \
--gisaid_metadata <insert metadata>
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Contributed by:
<<<<<<< HEAD
1.Arnold Lambisia
2.Sam Odoyo
3.Chimwemwe Mhango
4.Evalyne Nyambura
5.Daniel Omoding
======= +Arnold Lambisia +Sam Odoyo +Chimwemwe Mhango +Evalyne Nyambura +Daniel Omoding
>>>>>>> d6e9c83bd3dbbded98e5ec6f7f58903973006c9d