Parameters

A set of default parameters is provided, but these can be easily altered by either editing the params.config file, or by passing the new value when executing the workflow with nextflow. There are three main parameters in LMAS: ``–reference``, ``–fastq`` and ``–md``.

The reference sequences, in a single multifasta file, can be passed with the --reference parameter, and --fastq receives the raw data for assembly. The raw data is a collection of sequence fragments from the references and can be either obtained in silico or from real sequencing platforms. Users can pass text information, in a markdown file, on input samples to be presented in the report with the --md parameter.

Several options are available to alter the behaviour of the assemblers incorporated in LMAS, namely to alter the values of the k-mer for each assembly iteration. By default, these values reflect the corresponding default settings of the assemblers.

The target values for some quality assessment metrics can also be adjusted, such as N50 and NG50.

Input Files

fastq

Path expression to paired-end fastq files. Required.

  • Param: --fastq

  • Default: data/fastq/*_{1,2}.*

reference

Path to reference fasta file. Required.

  • Param: --reference

  • Default: data/reference/*.fasta

md

Path to markdown file with text to be displayed in the report. Optional.

  • Param: --md

  • Default: data/*.md

Assembly Quality Assessment

Minimum contig length

Value for minimum contig length, in basepairs.

  • Param: --minLength

  • Default: 1000

Mapped reads threshold

Value for the minimum percentage of a read length aligning to the contig to be considered as mapped.

  • Param: --mapped_reads_threshold

  • Default: 0.75

N Target

Target value for the N*x*, NA*x* and NG*x* metrics.

  • Param: --n_target

  • Default: 0.9

L Target

Target value for the L*x* metric.

  • Param: --l_target

  • Default: 0.5

L Target

Scale of x-axis for the L, NA and NG metrics plots.

  • Param: --plot_scale

  • Default: log

Assembler options

ABySS

  • Param: --abyss

  • Definition: Boolean controling the execution of the ABySS assembler.

  • Default: true

  • Param: --abyssKmerSize

  • Definition: K-mer size for the ABySS assembler, as an intiger.

  • Default: 96

  • Param: --abyssBloomSize

  • Definition: Bloom filter size for the ABySS assembler. It must be a sting with a value and an unit.

  • Default: 2G

GATB Minia Pipeline

  • Param: --gatb_minia

  • Definition: Boolean controling the execution of the GATB Minia Pipeline assembler.

  • Default: true

  • Param: --gatbKmerSize

  • Definition: K-mer sizes for the GATB Minia Pipeline assembler. It must be a sting with the values separated with a comma.

  • Default: ‘21,61,101,141,181’

  • Param: --gatb_besst_iter

  • Definition: Number of iteration during BESST scaffolding for the GATB Minia Pipeline assembler.

  • Default: 10000

  • Param: --gatb_error_correction

  • Definition: Boolean to control weather to skip error correction for the GATB Minia Pipeline assembler.

  • Default: false

IDBA-UD

  • Param: --idba

  • Definition: Boolean controling the execution of the IDBA-UD assembler.

  • Default: true

MetaHipMer2

  • Param: --metahipmer2

  • Definition: Boolean controling the execution of the MetaHipMer2 assembler.

  • Default: true

  • Param: --metahipmer2KmerSize

  • Definition: K-mer sizes for the MetaHipMer2 assembler. It must be a sting with the values separated with a comma.

  • Default: ‘21,33,55,77,99’

Minia

  • Param: --minia

  • Definition: Boolean controling the execution of the minia assembler.

  • Default: true

  • Param: --miniaKmerSize

  • Definition: K-mer size for the minia assembler, as an intiger.

  • Default: 31

MEGAHIT

  • Param: --megahit

  • Definition: Boolean controling the execution of the MEGAHIT assembler.

  • Default: true

  • Param: --megahitKmerSize

  • Definition: K-mer sizes for the MEGAHIT assembler. It must be a sting with the values separated with a comma.

  • Default: ‘21,29,39,59,79,99,119,141’

metaSPAdes

  • Param: --metaspades

  • Definition: Boolean controling the execution of the metaSPAdes assembler.

  • Default: true

  • Param: --metaspadesKmerSize

  • Definition: K-mer sizes for the metaSPAdes assembler. It must be a sting with ‘auto’ or with the values separated with a space.

  • Default: ‘auto’

SPAdes

  • Param: --spades

  • Definition: Boolean controling the execution of the SPAdes assembler.

  • Default: true

  • Param: --spadesKmerSize

  • Definition: K-mer sizes for the metaSPAdes assembler. It must be a sting with ‘auto’ or with the values separated with a space.

  • Default: ‘auto’

SKESA

  • Param: --skesa

  • Definition: Boolean controling the execution of the SKESA assembler.

  • Default: true

Unicycler

  • Param: --unicycler

  • Definition: Boolean controling the execution of the Unicycler assembler.

  • Default: true

VelvetOptimiser

  • Param: --velvetoptimiser

  • Definition: Boolean controling the execution of the VelvetOptimiser assembler.

  • Default: true

  • Param: --velvetoptimiser_hashs

  • Definition: Starting K-mer size for the VelvetOptimiser assembler, as an intiger.

  • Default: 19

  • Param: --velvetoptimiser_hashe

  • Definition: End K-mer size for the VelvetOptimiser assembler, as an intiger.

  • Default: 31

Execution Resources Parameters

CPUs

Number of CPUs for the assembly and mapping processes, as an intiger. This resource is double for each retry until max_cpus is reached.

  • Param: --cpus

  • Default: 8

Memory

Memory for the assembly and mapping processes, in the format of ‘value’.’unit’. This resource is double for each retry until max_memory is reached.

  • Param: --memory

  • Default: 32.Gb

Time

Time limit for the assembly and mapping processes, in the format of ‘value’.’unit’. This resource is double for each retry until max_time is reached.

  • Param: --memory

  • Default: 24.h

Max_cpus

Maximum number of CPUs for the assembly and mapping processes, as an intiger.

  • Param: --max_cpus

  • Default: 32

Max_memory

Maximum memory for the assembly and mapping processes, in the format of ‘value’.’unit’.

  • Param: --max_memory

  • Default: 100.Gb

Max_time

Maximum time for the assembly and mapping processes, in the format of ‘value’.’unit’.

  • Param: --max_memory

  • Default: 72.h