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config_ampliseq.yml
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config_ampliseq.yml
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#Please check the parameters, and adjust them according to your project needs.
# Project name
PROJECT: GENOMICON-Seq - Amplicon Sequencing
# =======================================================
# ================= GENERAL PARAMETERS ==================
# =======================================================
NUM_SAMPLES: 1
FRAG_REPLICATES: 1
NCORE: 8
SEED: "892"
OUTPUT_DIRECTORY: "/usr/src/app/pipeline/Output_data_ampliseq"
INPUT_DIRECTORY: "input_data_ampliseq"
FASTA_FILE: "HPV16.fa"
# =======================================================
# ================== SAMPLE PARAMETERS ==================
# =======================================================
# 1. GENOME TOPOLOGY - CIRCULAR/LINEAR
CIRCULAR: "Y"
# 2. GENOME COPIES IN THE SAMPLE
# ==============================
NR_COPIES: "1000"
MULTIFASTA_COPIES_TABLE: ""
# 3. MUTATION TARGETS
# ===================
MUT_CONTEXT: "ATC,CTA"
# 4. SUBSTITUTION TYPE
# ====================
TS_TV_RATIO: "3:1"
SUBSTITUTION_PROBABILITY_TABLE: ""
# 5. MUTATION MODE
# ================
# 5.a DETERMINISTIC MODE
# ======================
MUT_GENOME_FRACTION: ""
FRACTION_POSITION: ""
# 5.b SPECIFIC MUTATION RATE MODE
# ===============================
MUTATION_RATE: "1e-5"
# =============================================================
# ================== FRGMENTATION PARAMETERS ==================
# =============================================================
FRAGMENT_FRACTION: "1"
FRAGMENT_LENGTH: "250:550"
# ====================================================
# ================== PCR PARAMETERS ==================
# ====================================================
PRIMERS: "all_primers.csv"
NUM_PCR: 2
AMPLICON_LENGTH: 250
NUM_CYCLES: "25"
POL_ERROR_RATE: "1e-5"
FRACTION_PCR_SEQUENCING: "0.005"
# ADVANCED PCR PARAMETERES
# ========================
K_PARAMETER_pcr: "1"
MIDPOINT_CYCLE: ""
# ==========================================================
# ================= SEQUENCING PARAMETERS ==================
# ==========================================================
NUM_READS: "100000"
MODE: ""
ERROR_MODEL: "novaseq"
FASTA_GZ_OUTPUT: "--compress"
GC_BIAS: "--gc_bias"
OPT_FRAG_LENGTH: "NO"
# ADVANCED SEQUENCING PARAMETER
# =============================
K_PARAMETER_seq: "0.005"