CulebrONT 1.5.2 report
CulebrONT is a Snakemake workflow available on github created by:
J.Orjuela (IRD), A.Comte (IRD), T.V Bao (IRD), S.Ravel (CIRAD), F.Charriat (CIRAD), F.Sabot (IRD) and S.Cunnac (IRD)
Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and GPLv3.
Intellectual property belongs to IRD and authors
For more quality outputs you can check in the quality output directory.
Tools used in this report:
- BUSCO : https://busco.ezlab.org/
- QUAST : http://quast.sourceforge.net/quast
- BLOBTOOLS: https://blobtools.readme.io/docs
- ASSEMBLYTICS: http://assemblytics.com/
- SAMTOOLS FLAGSTATS : http://www.htslib.org/doc/samtools-flagstat.html
- KAT : https://github.com/TGAC/KAT
Rulegraph
Config file Parameters
Click to open and see Config file
DATA:
FASTQ: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/fastq/
FAST5: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/fast5/
ILLUMINA: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/illumina/
GENOME_SIZE: 4.8m
REF: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/ref/BAI3_Sanger.fsa
OUTPUT: /home/comte/Documents/IPME/CulebrONT_pipeline/CulebrONT_OUTPUT/
ASSEMBLY:
CANU: true
FLYE: true
MINIASM: true
RAVEN: true
SMARTDENOVO: true
SHASTA: true
POLISHING:
RACON: true
CIRCULAR: true
CORRECTION:
NANOPOLISH: true
MEDAKA: true
PILON: true
FIXSTART: true
QUALITY:
BUSCO: true
QUAST: true
BLOBTOOLS: true
ASSEMBLYTICS: true
FLAGSTATS: true
KAT: true
MSA:
MAUVE: true
params:
MINIMAP2:
PRESET_OPTION: map-ont
FLYE:
OPTIONS: ''
CANU:
OPTIONS: gridOptions="-p long" useGrid=true
SMARTDENOVO:
KMER_SIZE: 16
OPTIONS: -J 5000
SHASTA:
MEM_MODE: filesystem
MEM_BACKING: disk
OPTIONS: --Reads.minReadLength 0
CIRCLATOR:
OPTIONS: ''
RACON:
RACON_ROUNDS: 2
CORRECTION_MAKERANGE:
SEGMENT_LEN: '50000'
OVERLAP_LEN: '200'
NANOPOLISH:
OPTIONS: ''
MEDAKA:
MEDAKA_TRAIN_WITH_REF: false
MEDAKA_MODEL_PATH: r941_min_high_g303
MEDAKA_FEATURES_OPTIONS: --batch_size 10 --chunk_len 100 --chunk_ovlp 10
MEDAKA_TRAIN_OPTIONS: '--batch_size 10 --epochs 500 '
MEDAKA_CONSENSUS_OPTIONS: '--batch 200 '
PILON:
PILON_ROUNDS: 2
OPTIONS: ''
BUSCO:
DATABASE: 'bacteria_odb10 --update-data '
MODEL: genome
SP: ''
QUAST:
GFF: ''
OPTIONS: --large
GENOME_SIZE_PB: 4800000
DIAMOND:
DATABASE: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/testBacteria.dmnd
MUMMER:
MINMATCH: 100
MINCLUSTER: 500
ASSEMBLYTICS:
UNIQUE_ANCHOR_LEN: 10000
MIN_VARIANT_SIZE: 50
MAX_VARIANT_SIZE: 10000
BLOBTOOLS:
NAMES: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/blobtools/names.dmp
NODES: /home/comte/Documents/IPME/CulebrONT_pipeline/Data-Xoo-sub/blobtools/nodes.dmp
Benchmark
The average run time of each tool in second.
5percentB1-1
BUSCO
BUSCO sets are collections of orthologous groups with near-universally-distributed single-copy genes in each species
5percentB1-1
QUAST
QUAST is a good starting point to help evaluate the quality of assemblies. It provides many helpful contiguity statistics.
5percentB1-1
BLOBTOOLS
5percentB1-1
CANU
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
FLYE
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
MINIASM
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
RAVEN
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SMARTDENOVO
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SHASTA
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
ASSEMBLYTICS
5percentB1-1
CANU
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
FLYE
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
MINIASM
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
RAVEN
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SMARTDENOVO
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SHASTA
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
KAT
5percentB1-1
CANU
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
FLYE
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
MINIASM
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
RAVEN
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SMARTDENOVO
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
SHASTA
STEP_CORRECTION_NANOPOLISH_STARTFIXED
STEP_CORRECTION_MEDAKA_STARTFIXED
STEP_CORRECTION_PILON_STARTFIXED
FLAGSTATS
SAMTOOLS FLAGSTATS was used to calculate remapping between illumina reads and each last assembler.