This pipeline assembles Illumina paired end reads. It results in a scaffold and annotated assembly.
Steps:
-Read trimming
-SPades de novo assembly
-Coverage selection (exclusion of scaffold with low coverage)
-Prokka annotation
#Requirements:
-Linux 64 bit system
-python (version 2.7)
-SPAdes (version 3.10.1)
-samtools (version 1.3)
-prokka (version 1.12)
-bowtie2 (version 2.3.0)
#Installation:
wget https://github.com/danielwuethrich87/Bacterial_genome_assembly/archive/master.zip
unzip master.zip
#Usage:
sh bacteria_assembly.sh <Sample_ID> <Reads_R1> <Reads_R2> <Genus_> <species_> <Number_of_cores>
<Sample_ID> Unique identifier for the sample
<Reads_R1> Foreward read file
<Reads_R2> Reversed read file
<Genus_> Genus name of the bacterial species
<species_> Species name of the bacterial species
<Number_of_cores> number of parallel threads to run (int)
#example:
#!/bin/sh
#$ -q all.q
#$ -e $JOB_ID.cov.err
#$ -o $JOB_ID.cov.out
#$ -cwd
#$ -pe smp 24
module add UHTS/Assembler/SPAdes/3.10.1;
module add UHTS/Analysis/samtools/1.3;
module add UHTS/Analysis/prokka/1.12;
module add UHTS/Aligner/bowtie2/2.3.0;
for i in FAM22234
do
sh /home/dwuethrich/Application/assembly_pipeline/bacteria_assembly.sh "$i" ../../reads/"$i"_R1.fastq.gz ../../reads/"$i"_R2.fastq.gz Pediococcus acidilactici "$NSLOTS"
done