project_name        ECOLI_IS220_QUAKE_1K
output_dir          ./spades_output/ECOLI_IS220_QUAKE_1K
output_to_console   true
developer_mode      false
compilation_dir     ./teamcity_precompiled/ECOLI_IS220_QUAKE_1K

dataset
{
    paired_reads        $cfg/../../../test_dataset/ecoli_1K_1.fq.gz $cfg/../../../test_dataset/ecoli_1K_2.fq.gz
    single_cell         false
}

assembly
{
    iterative_K         21 55
    paired_mode         true
    generate_sam_files  true
}

quality_assessment
{
    reference           $cfg/../../../test_dataset/reference_1K.fa.gz
    genes               $cfg/../../../test_dataset/genes_1K.gff
    operons             $cfg/../../../test_dataset/operons_1K.gff
}
