example.assess.input

#path to assemblies
path2fastas=/PATH/TO/FASTAS
fasta=( assembly1.fasta assembly2.fasta assembly3.fasta )

#read info
read_path=/PATH/TO/CLEANED/READS
sample=( sampleID ) #assumes reads are named: <sample>.pair1.fastq.gz, <sample>.pair2.fastq.gz, <sample>.single.fastq.gz

#misc
threads=6
platform=Illumina

#reference sequence
ref=/PATH/TO/REFERENCE/reference.fasta

#cegma protein fasta
cegma=/PATH/TO/CEGMA/PROTEINS/CEGMA.proteins.fa

#assemblathon script info
thon_path=/PATH/TO/assemblathon2-analysis
export PERL5LIB=/PATH/TO/assemblathon2-analysis

#cegma info
export CEGMA=/usr/local/bin/cegma_v2.4.010312/
export WISECONFIGDIR=/usr/local/bin/wise2.2.3-rc7/wisecfg
export PATH=$PATH:/usr/local/bin/hmmer-3.0-linux-intel-x86_64/binaries:/usr/local/bin/cegma_v2.4.010312/bin/
export PERL5LIB=$PERL5LIB:/usr/local/bin/cegma_v2.4.010312/lib

##your email address to notify you when the script finishes
email=name@domain.edu