project_name        ECOLI_IS480_QUAKE
output_dir          ./spades_output/ECOLI_IS480_QUAKE
output_to_console   true
developer_mode      true
compilation_dir     ./teamcity_precompiled/ECOLI_IS480_QUAKE

dataset
{
    paired_reads             $cfg/../../../data/input/E.coli/is480/ERR022075_1.cor.fastq.gz $cfg/../../../data/input/E.coli/is480/ERR022075_2.cor.fastq.gz
    single_reads             $cfg/../../../data/input/E.coli/is480/ERR022075_1.cor_single.fastq.gz $cfg/../../../data/input/E.coli/is480/ERR022075_2.cor_single.fastq.gz
    single_cell              false
}

assembly
{
    iterative_K         21 33 55
    paired_mode         true
    generate_sam_files  true
}

quality_assessment
{
    reference           $cfg/../../../data/input/E.coli/MG1655-K12.fasta.gz
    genes               $cfg/../../../data/input/E.coli/genes/genes.gff
    operons             $cfg/../../../data/input/E.coli/genes/operons.gff
}
