arnoldlambisia / denv_phylo

This is a repository generated during the workflows training at KWTRP for DENV phylogentics

#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

##Pipeline

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:

1. 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.

2. Alignment of subsampled fasta sequences using nextalign

The reference used is NC_001477 polyprotein for Dengue 1.

3. Maximum likelihood tree genration using iqtree

parameters used: -m TEST -bb 1000 -T 4

4. Creation of a time resolved tree using treetime

###Usage

The pipeline can be run suing the following command:

<<<<<<< HEAD
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>
>>>>>>> d6e9c83bd3dbbded98e5ec6f7f58903973006c9d

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