This pipeline is designed by team1-group1, to assemble genomes from PE Illumina reads using a number of assembly programs. This pipeline is used to generate final result.
This pipeline is based on python3 and requires pandas and numpy.
This pipeline also requires these software are installed and can be found in PATH(depends on which one you want to use).
ABYSS(optional)
SPAdes(optional)
SEKSA(optional)
MaSuRCA(optional)
git clone https://github.gatech.edu/compgenomics2019/Team1-GenomeAssembly.git
cd Team1-GenomeAssembly
python3 assemble_pipeline_g1.py -i dataset/f1.fq.gz dataset/f2.fq.gz -a spades -o scaffolds.fa
--trimmomatic specify trimmomatic jar file here if you do not want to use the one in bin/
-a declare which assembler to use, if given multiple, then the best is used as output
-i file1 file2 pair end input files.
-t tmp folder. please be careful because tmp will be cleared when pipeline starts.
-n number of threads to use in trimming
-o output file name
-k if you do not set this, tmp is cleared when pipeline finishes
--skip-crop trimmomatic will not do HEADCROP and CROP if this flag is set
--trim-only assemble steps are skip if this is set, if you want to keep trim result please set -k
--assemble-only trim steps are skip if this is set
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Input file must be gzipped fastq file, fastq file can be fetched from NCBI using SRAToolkit.
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This pipeline is designed to process one sample, if you have many samples, please run this pipeline multiple times. Please specify different tmp folder for each sample, otherwise tmp files could mess up.
Developed by Hanying Pan([email protected]).