Genome Assembly Benchmark Toolkit
To install Genome Assembly Benchmark Toolkit, you must have a minimum of 6 GiB free disk space and minimum of 16 GiB free RAM to test run.
To provide an easier way to install, we provide a miniconda based installer.
Installation also requires pre-instaled git, gcc, cpp and zlib1g-dev.
git clone https://github.com/sarangian/gabtk.git
cd gabtk
chmod 755 install.sh
./install.sh
Post Installation Instructions
After successful installation, close the current terminal.
In a new terminal. source the bashrc file: source ~/.bashrc
Activate gabtk environment using command: conda activate
Prepare a Project for Benchmark Analysis
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The directory from which which the benchmark.py script will be fired, must contain the luigi.cfg template file
.. code-block:: none
[core]
default-scheduler-port:0000
error-email=
[GlobalParameter]
projectName=
assembly_name=i
projectDir=
adapter=
domain=
pe_read_dir=
mp_read_dir=
ont_read_dir=
pac_read_dir=
pe_read_suffix=
mp_read_suffix=
genome_size=
ont_read_suffix=
pac_read_suffix=
threads=
maxMemory=
seq_platforms=
.. code-block:: none
benchmark.py configureProject --help
benchmark.py configureProject --projectName Illumina_PE_Benchmark \
--cpus 8 \
--maxMemory 16 \
--domain prokaryote \
--dataDir /home/user/Documents/genome_assembly_benchmark/data/ \
--genomeName ecoli \
--genomeSize 4600000 \
--schedulerPort 8082 \
--userEmail [email protected] \
--outDir raw_data_symlink \
--local-scheduler
The configureProject command will generate the (1) luigi.cfg file (2) outDir folder containg the symbolic link to the raw fastq files present in raw_data_symlink folder (3) sample_list folder containing 4 files (i) pe_samples.lst (ii)mp_samples.lst (iii) ont_samples.lst (iv) pac_samples.lst
Example of a luigi.cfg file generated using configureProject command
.. code-block:: none
[core]
default-scheduler-port:8082
[email protected]
[GlobalParameter]
projectName=LongReadAssembly
assembly_name=ecoli
projectDir=/home/adityans/Documents/genome_assembly_benchmark/PEMP_Benchmark/
adapter=/home/adityans/Documents/genome_assembly_benchmark/tasks/utility/adapters.fasta.gz
domain=prokaryote
pe_read_dir=/home/adityans/Documents/genome_assembly_benchmark/raw_data_symlink/pe/
mp_read_dir=/home/adityans/Documents/genome_assembly_benchmark/raw_data_symlink/mp/
ont_read_dir=/home/adityans/Documents/genome_assembly_benchmark/raw_data_symlink/ont/
pac_read_dir=/home/adityans/Documents/genome_assembly_benchmark/raw_data_symlink/pacbio/
pe_read_suffix=fq.gz
mp_read_suffix=fq.gz
genome_size=4600000
ont_read_suffix=fq.gz
pac_read_suffix=fastq.gz
threads=4
maxMemory=12
seq_platforms=pe-pac
QC Analysis ^^^^^^^^^^^
.. code-block:: none
benchmark.py rawReadsQC --help
--seq-platforms Choose From[pe: paired-end,
pe-mp: paired-end and mate-pair,
pe-ont: paired-end and nanopore,
pe-pac: paired-end and pacbio, ont: nanopore, pac: pacbio]
Choices: {pe, pe-mp, pe-ont, pac, ont}
Example 1: paired-end reads QC Analysis
benchmark.py rawReadsQC \
--seq-platforms pe \
--local-scheduler
Example 2: paired-end and mate-pair reads QC Analysis
benchmark.py rawReadsQC \
--seq-platforms pe-mp \
--local-scheduler
Example 3: paired-end and pacbio reads QC Analysis
benchmark.py rawReadsQC \
--seq-platforms pe-pac \
--local-scheduler
.. code-block:: none
benchmark.py cleanReads <arguments> --local-scheduler
arguments type Description
Mandetory parameter
--seq_platforms str choose from [
pe: paired-end,
pe-mp: paired-end and mate-pair,
pe-ont: paired-end and nanopore,
pe-pac: paired-end and pacbio,
ont: nanopore,
pac: pacbio]
optional parameters
--cleanFastq-kmer-length int Kmer length used for finding contaminants.
Contaminants shorter than kmer length will not be found.
Default 21
--cleanFastq-corret-error Bool Perform Error Correction Or Not
[Choose from True or False]
Default: False
--cleanFastq-k-trim str Trimming protocol to remove bases matching
reference kmers from reads
Choose From[f: dont trim, r: trim to right, l: trim to left]
Default: r
--cleanFastq-quality-trim str Trimming protocol to remove bases with quality below the minimum
average region quality from read ends. Performed after looking for kmers. If enabled, set also Average quality below which to trim region.
Choose From [f: trim neither end',
rl: trim both end,
r: trim only right end,
l: trim only left end]
Default: lr
--cleanFastq-min-GC float Discard reads with GC content below this.
Default: min_gc=0.0
--cleanFastq-max-GC float Discard reads with GC content below this.
Default: max_gc=1.0
--cleanFastq-kmer-length int Kmer length used for finding contaminants.
Default: kmer=13
--cleanFastq-trim-front int Number of bases to be trimmed in front for read.
Default: 0
--cleanFastq-trim-tail int trimming how many bases from the end of read.
Default: 0
--cleanFastq-max-n int Maximum number of Ns after trimming
If non-negative, reads with more Ns than this (after trimming) will be discarded.
Default: -1
--cleanFastq-trim-quality int Average quality below which to trim region
Default: 6
--cleanFastq-min-length int Reads shorter than min_length will be discarded
Default: 40
--cleanFastq-min-average-quality int Reads with average quality (after trimming) below this will be discarded
Default: 10
--cleanFastq-min-base-quality int Reads with any base below this quality (after trimming) will be discarded
Default: 0
--cleanFastq-long-read-min-length int This parameter is specific for long read (pacbio / nanopore )only
seq_platforms='pac or ont'].
Reads shorter than min_length will be discarded.
Default: long_read_min_length=1000
--cleanFastq-long-read-mean-quality int This parameter is specific for long read only.
The mean quality is the mean read identity as indicated by the Phred quality scores. Example:
example, consider a read where all the fastq quality characters are +. The qscores for each base are 10 whichequates to a 90 percentage chance of being correct. This read would then have a mean quality score of 90. Read mean qualities are converted to a z-score and scaled to the range 0-100 to make the mean qality score. This means that the read with the worst mean quality in the input set will get a mean quality score of 0 and the read with the best mean quality will get a mean quality score of 100. Default:
meanQ=80
--cleanFastq-long-read-keep-percent int This parameter is specific for long read only.
The percentage of the best reads to be retained.
Default: keep_percent=90
--local-scheduler
.. code-block:: none
benchmark.py correctPAC <arguments> --local-scheduler
Mandetory Arguments
--pre-process-reads str Choose [yes or no]
Example
benchmark.py correctPAC --pre-process-reads yes --local-scheduler
.. code-block:: none
Mandetory Arguments
--pre-process-reads str Choose [yes or no]
benchmark.py correctONT --pre-process-reads yes --local-scheduler
Genome Assembly ^^^^^^^^^^^^^^^
.. code-block:: none
Note: skesa is used for assembling prokaryotic Illumina paired-end reads only
Mandetory Arguments
--pre-process-reads str Choose [yes or no]
Optional Argument
--kmer int Minimal Kmer length for assembly
Default: 21
--steps int Number of assembly iterations from minimal to maximal kmer length in reads
Default: 11
--min-contig-length int Exclude contigs from the FASTA file which are shorter than this length.
Default: 200
Example: run skesa assembler
.. code-block:: none
case 1: running skesa with out read cleaning
benchmark.py skesa --pre-process-read no --min-contig-length 500 --local-scheduler
case 2: running skesa with read cleaning parameters
benchmark.py skesa \
--pre-process-read yes \
--min-contig-length 500 \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Note: lightAssembler is used for assembling Illumina paired-end reads only
Mandetory Arguments
--pre-process-reads str Choose [yes or no]
Optional Argument
--kmer int Minimal Kmer length for assembly
**Example: run light assembler**
.. code-block:: none
case 1: running lightassembler with out read cleaning
benchmark.py lightAssembler --pre-process-read no --local-scheduler
case 2: running lightassembler with read cleaning parameters
benchmark.py lightAssembler \
--pre-process-read yes \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Note: discovardenovo is used for assembling Illumina paired-end reads only
Mandetory Arguments --pre-process-reads str Choose [yes or no]
Optional Argument --kmer int Minimal Kmer length for assembly
Example: run discovardenovo assembler
.. code-block:: none
case 1: running discovardenovo with out read cleaning
benchmark.py discovardenovo --pre-process-read no --local-scheduler
case 2: running discovardenovo with read cleaning parameters
benchmark.py discovardenovo \
--pre-process-read yes \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Note: sparseAssembler is used for assembling Illumina paired-end or paired-end with mate-pair reads only
Mandetory Arguments
--pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [pe:paired-end, pe-mp: paired-end and mate-pair]
Optional Argument
--kmer int Minimal Kmer length for assembly
Example: run sparse assembler
.. code-block:: none
case 1: running sparseAssembler with out read cleaning
benchmark.py sparseAssembler --pre-process-read no --local-scheduler
case 2: running sparseAssembler with read cleaning parameters
benchmark.py sparseAssembler \
--pre-process-read yes \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [pe:paired-end, pe-mp: paired-end and mate-pair pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Optional Argument --kmer str comma separated list of kmers. must be odd and less than 128. Default: auto
--cov-cutoff str coverage cutoff value (a positive float number, or 'auto', or 'off'). Default 'off'
Example: run spades assembler
.. code-block:: none
case 1: running spades with out read cleaning
benchmark.py spades --pre-process-read no --spades-seq-platforms pe-pac --local-scheduler
case 2: running spades with read cleaning parameters
benchmark.py spades \
--pre-process-read yes \
--spades-seq-platforms pe-pac \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [pe:paired-end, pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Optional Argument --mode str Choose From[ normal: moderate contig size and misassembly rate conservative: smaller contigs lowest misassembly rate bold: longest contigs higher misassembly rate]
--min-contig-length int Exclude contigs from the FASTA file which are shorter than this length. Default: 200
Example: run unicycler assembler
.. code-block:: none
case 1: running unicycler with out read cleaning
benchmark.py unicycler --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running unicycler with read cleaning parameters
benchmark.py unicycler \
--pre-process-read yes \
--seq-platforms pe-pac \
--mode normal \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [pe: paired-end, pe-mp: paired-end and mate-pair pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
--pe-frag-mean float Illumina paired-end fragment mean
--pe-frag-sd float Illumina paired-end fragment sd
--mp-frag-mean float Illumina mate-pair reads mean optional --in case of paired-end read only assembly
--mp-frag-sd float lumina mate-pair reads sd optional --in case of paired-end read only assembly
Example: run masurca assembler
.. code-block:: none
NOTE: currently running masurca assembler through the gabtk pipeline supports only one paired-end and (or)
only one mate-pair library. i.e multipe read libraries are not supported
masurca assembler does not require read cleaning.
Case 1: running masurca assembler with one paired-end read library and one pacbio read library
benchmark.py masurca \
--seq-platforms pe-pac \
--pe-frag-mean 180 \
--pe-frag-sd 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [ pe: paired-end pe-mp: paired-end and mate-pair pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Example: run ray assembler
.. code-block:: none
case 1: running ray with out read cleaning
benchmark.py ray --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running ray with read cleaning parameters
benchmark.py ray \
--pre-process-read yes \
--seq-platforms pe-pac \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ pe: paired-end pe-mp: paired-end and mate-pair pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Example: run idba assembler
.. code-block:: none
case 1: running idba with out read cleaning
benchmark.py idba --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running idba with read cleaning parameters
benchmark.py idba \
--pre-process-read yes \
--seq-platforms pe-pac \
--cleanFastq-min-average-quality 20 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [ pe: paired-end pe-mp: paired-end and mate-pair pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Example: run abyss assembler
.. code-block:: none
case 1: running abyss with out read cleaning
benchmark.py abyss --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running abyss with read cleaning parameters
benchmark.py abyss \
--pre-process-read yes \
--seq-platforms pe-pac \
--cleanFastq-min-average-quality 20 \
--cleanFastq-long-read-mean-quality 70 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [ pe-ont: paired-end and nanopore pe-pac: paired-end and pacbio]
Example: run haslr assembler
.. code-block:: none
case 1: running haslr with out read cleaning
benchmark.py haslr --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running haslr with read cleaning parameters
benchmark.py haslr \
--pre-process-read yes \
--seq-platforms pe-pac \
--cleanFastq-min-average-quality 20 \
--cleanFastq-long-read-mean-quality 70 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [ pe: paired-end pe-mp: paired-end and mate-pair]
--max-read-len int Maximum read length --avg-pe-ins float paired-end reads average insert size --avg-me-ins float mate-paired reads average insert size --min-contig-length int minimum contig length
Example: run soapdenovo assembler
.. code-block:: none
case 1: running soapdenovo with out read cleaning
benchmark.py soapdenovo --pre-process-read no --seq-platforms pe-pac --local-scheduler
case 2: running soapdenovo with read cleaning parameters (read library: paired-end)
benchmark.py soapdenovo \
--pre-process-read yes \
--seq-platforms pe \
--cleanFastq-min-average-quality 20 \
--max-read-len 150 \
--avg-pe-ins 180 \
--min-contig-length 200 \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads str Choose [yes or no]
--seq-platforms str Choose [ ont: nanopore pac: pacbio]
Optional Arguments --dbg-assembler str Choose [ light: LightAssembler sparse: SparseAssembler minia: MiniaAssembler] Default: sparse
Example: run dbg2olc assembler
.. code-block:: none
case 1: running dbg2olc with out read cleaning
benchmark.py dbg2olc --pre-process-read no --seq-platforms pac --local-scheduler
case 2: running dbg2olc with read cleaning parameters
benchmark.py dbg2olc \
--pre-process-read yes \
--seq-platforms pac \
--cleanFastq-min-average-quality 20 \
--dbg-assembler sparse \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platform str Choose [ ont: nanopore pac: pacbio] Optional Arguments --min-contig-size int Default: 500
benchmark.py smartdenovo
--pre-process-read yes
--seq-platforms pac
--cleanFastq-min-average-quality 20
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ pacbio-raw: pacbio raw pacbio-corr: pacbio corrected nano-raw: nanopore raw nano-corr: nanopore corrected]
Example: run flye assembler
.. code-block:: none
case 1: running flye with out read cleaning
benchmark.py flye --pre-process-read no --seq-platforms pacbio-raw --local-scheduler
case 2: running flye with read cleaning parameters
benchmark.py flye \
--pre-process-read yes \
--seq-platforms pacbio-raw \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ pacbio-raw: pacbio raw pacbio-corr: pacbio corrected nano-raw: nanopore raw nano-corr: nanopore corrected]
Example: run canu assembler
.. code-block:: none
case 1: running canu with out read cleaning
benchmark.py canu --pre-process-read no --seq-platforms pacbio-raw --local-scheduler
case 2: running canu with read cleaning parameters
benchmark.py canu \
--pre-process-read yes \
--seq-platforms pacbio-raw \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
Optional Argument --seq-platform str Default: pac
Example: run mecat2 assembler Note: Read type must be pacbio
.. code-block:: none
case 1: running mecat2 with out read cleaning
benchmark.py mecat2 --pre-process-read no --local-scheduler
case 2: running mecat2 with read cleaning parameters
benchmark.py mecat2 \
--pre-process-read yes \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
Optional Argument --seq-platform str Default: ont
Example: run necat assembler Note: Read type must be nanopore
.. code-block:: none
case 1: running necat with out read cleaning
benchmark.py necat --pre-process-read no --local-scheduler
case 2: running necat with read cleaning parameters
benchmark.py neact \
--pre-process-read yes \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platform str Choose [ pac: pacbio ont: nanopore]
Example: run abruijn assembler
.. code-block:: none
case 1: running abruijn with out read cleaning
benchmark.py abruijn --pre-process-read no --seq-platform pacbio --local-scheduler
case 2: running abruijn with read cleaning parameters
benchmark.py abruijn \
--seq-platform pacbio \
--pre-process-read yes \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ pac: pacbio ont: nanopore]
Example: run abruijn assembler
.. code-block:: none
case 1: running wtdbg2 with out read cleaning
benchmark.py wtdbg2 --pre-process-read no --seq-platform pac --local-scheduler
case 2: running abruijn with read cleaning parameters
benchmark.py wtdbg2 \
--seq-platform pac \
--pre-process-read yes \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ pac: pacbio ont: nanopore]
Example: run abruijn assembler
.. code-block:: none
case 1: running miniasm with out read cleaning
benchmark.py miniasm --pre-process-read no --seq-platform pac --local-scheduler
case 2: running miniasm with read cleaning parameters
benchmark.py miniasm \
--seq-platform pac \
--pre-process-read yes \
--local-scheduler
.. code-block:: none
Mandetory Arguments --pre-process-reads strs Choose [yes or no]
--seq-platforms str Choose [ nanopore pacbio] Optional Arguments --min-contig-length int Default: 500