INNUca - Reads Control and Assembly
INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
https://github.com/B-UMMI/INNUca
- Illumina paired-end reads (paired end information: sampleName_R1_001 / sampleName_R2_001 OR sampleName_1 / sampleName_2) (gzip compressed: .fastq.gz or .fq.gz)
- Expected species name
- Expected genome size in Mb
Mandatory
- Java JDK
- mlst (https://github.com/tseemann/mlst) >= v2.4 (whenever mlst module should run) (it is recommended to use a mlst version with updated databases)
- ReMatCh (https://github.com/B-UMMI/ReMatCh) >= v3.2 (whenever true coverage module should run)
- gzip >= v1.6 (normally found in Linux OS)
Optional
(executables are provided, but user's own executables can be used with --doNotUseProvidedSoftware option)
- Bowtie2 >= v2.2.9
- Samtools = v1.3.1
- FastQC = v0.11.5
- Trimmomatic = v0.36 (make sure the .jar file is executable and it is in your PATH)
- Pear = v0.9.10
- SPAdes >= v3.9.0
- Pilon = v1.18
git clone https://github.com/B-UMMI/INNUca.git
usage: INNUca.py [-h] [--version]
-s "Streptococcus agalactiae" -g 2.1
(-i /path/to/input/directory/ | -f /path/to/input/file_1.fq.gz /path/to/input/file_2.fq.gz)
[-o /output/directory/] [-j N]
[--jarMaxMemory 10] [--doNotUseProvidedSoftware]
[--keepIntermediateAssemblies]
[--skipEstimatedCoverage] [--skipFastQC]
[--skipTrimmomatic] [--skipSPAdes] [--skipAssemblyMapping]
[--skipPilon] [--skipMLST] [--runPear] [--noLog] [--noGitInfo]
[--skipTrueCoverage | --trueConfigFile species.config]
[--adapters adaptersFile.fasta | --doNotSearchAdapters]
[--estimatedMinimumCoverage N]
[--fastQCkeepFiles] [--fastQCproceed]
[--doNotTrimCrops | [[--trimCrop N] [--trimHeadCrop N]]]
[--trimSlidingWindow window:meanQuality] [--trimLeading N]
[--trimTrailing N] [--trimMinLength N] [--trimKeepFiles]
[--pearKeepFiles] [--pearMinOverlap N]
[--spadesVersion] [--spadesNotUseCareful]
[--spadesMinContigsLength N] [--spadesMaxMemory N]
[--spadesMinCoverageAssembly 10] [--spadesMinKmerCovContigs N]
[--spadesKmers 55 77 [55 77 ...] | --spadesDefaultKmers]
[--assemblyMinCoverageContigs N]
[--maxNumberContigs N] [--saveExcludedContigs]
[--pilonKeepFiles]
INNUca - Reads Control and Assembly
optional arguments:
-h, --help show this help message and exit
--version Version information
Required options:
-s "Streptococcus agalactiae", --speciesExpected "Streptococcus agalactiae"
Expected species name (default: None)
-g 2.1, --genomeSizeExpectedMb 2.1
Expected genome size in Mb (default: None)
Required INPUT options (one of the following):
-i /path/to/input/directory/, --inputDirectory /path/to/input/directory/
Path to directory containing the fastq files. Can be
organized in separete directories by samples or all
together (default: None)
-f /path/to/input/file_1.fq.gz /path/to/input/file_2.fq.gz, --fastq /path/to/input/file_1.fq.gz /path/to/input/file_2.fq.gz
Path to Pair-End Fastq files (default: None)
General options:
-o /output/directory/, --outdir /output/directory/
Path for output directory (default: .)
-j N, --threads N Number of threads (default: 1)
--jarMaxMemory 10 Sets the maximum RAM Gb usage by jar files
(Trimmomatic and Pilon). Can also be auto or off. When
auto is set, 1 Gb per thread will be used up to the
free available memory (default: off)
--doNotUseProvidedSoftware
Tells the software to not use FastQC, Trimmomatic,
SPAdes, Bowtie2, Samtools and Pilon that are provided
with INNUca.py (default: False)
--keepIntermediateAssemblies
Tells INNUca to keep all the intermediate assemblies
(default: False)
--skipEstimatedCoverage
Tells the programme to not estimate coverage depth
based on number of sequenced nucleotides and expected
genome size (default: False)
--skipTrueCoverage Tells the programme to not run trueCoverage_ReMatCh
analysis (default: False)
--skipFastQC Tells the programme to not run FastQC analysis
(default: False)
--skipTrimmomatic Tells the programme to not run Trimmomatic (default:
False)
--skipSPAdes Tells the programme to not run SPAdes and consequently
Pilon correction, Assembly Mapping check and MLST
analysis (SPAdes contigs required) (default: False)
--skipAssemblyMapping
Tells the programme to not run Assembly Mapping check
(default: False)
--skipPilon Tells the programme to not run Pilon correction and
consequently Assembly Mapping check (bam files
required) (default: False)
--skipMLST Tells the programme to not run MLST analysis (default:
False)
--runPear Tells the programme to run Pear (default: False)
--noLog Do not create a log file (default: False)
--noGitInfo Do not retreive GitHub repository information
(default: False)
Adapters options (one of the following):
--adapters adaptersFile.fasta
Fasta file containing adapters sequences to be used in
FastQC and Trimmomatic (default: None)
--doNotSearchAdapters
Tells INNUca.py to not search for adapters and clip
them during Trimmomatic step (default: False)
Estimated Coverage options:
--estimatedMinimumCoverage N
Minimum estimated coverage to continue INNUca pipeline
(default: 15)
trueCoverage_ReMatCh options:
--trueConfigFile species.config
File with trueCoverage_ReMatCh settings. Some species
specific config files can be found in
INNUca/modules/trueCoverage_rematch/ folder. Use those
files as example files. For species with config files
in INNUca/modules/trueCoverage_rematch/ folder (not
pre releases versions, marked with "pre."),
trueCoverage_ReMatCh will run by default, unless
--skipTrueCoverage is specified. Do not use together
with --skipTrueCoverage option (default: None)
FastQC options:
--fastQCkeepFiles Tells INNUca.py to not remove the output of
FastQC (default: False)
--fastQCproceed Do not stop INNUca.py if sample fails FastQC (default:
False)
Trimmomatic options:
--doNotTrimCrops Tells INNUca.py to not cut the beginning and end of
reads during Trimmomatic step (unless specified with
--trimCrop or --trimHeadCrop, INNUca.py will search
for nucleotide content bias at both ends and will cut
by there) (default: False)
--trimCrop N Cut the specified number of bases to the end of the
maximum reads length (default: None)
--trimHeadCrop N Trimmomatic: cut the specified number of bases from
the start of the reads (default: None)
--trimSlidingWindow window:meanQuality
Trimmomatic: perform a sliding window trimming,
cutting once the average quality within the window
falls below a threshold (default: 5:20)
--trimLeading N Trimmomatic: cut bases off the start of a read, if
below a threshold quality (default: 3)
--trimTrailing N Trimmomatic: cut bases off the end of a read, if below
a threshold quality (default: 3)
--trimMinLength N Trimmomatic: drop the read if it is below a specified
length (default: 55)
--trimKeepFiles Tells INNUca.py to not remove the output of
Trimmomatic (default: False)
Pear options:
--pearKeepFiles Tells INNUca.py to not remove the output of Pear
(default: False)
--pearMinOverlap Minimum nucleotide overlap between read pairs for Pear
assembly them into only one read (default: 2/3 of maximum
reads length or 33 whenever is was not possible to determine
it with FastQC)
SPAdes options:
--spadesVersion 3.11.0
Tells INNUca.py which SPAdes version to use
(available options: 3.9.0, 3.10.1, 3.11.0) (default:
3.11.0)
--spadesNotUseCareful
Tells SPAdes to only perform the assembly without the
--careful option (default: False)
--spadesMinContigsLength N
Filter SPAdes contigs for length greater or equal than
this value (default: maximum reads size or 200 bp)
--spadesMaxMemory N The maximum amount of RAM Gb for SPAdes to use
(default: 2 Gb per thread will be used up to the free
available memory)
--spadesMinCoverageAssembly 10
The minimum number of reads to consider an edge in the
de Bruijn graph during the assembly. Can also be auto
or off (default: 2)
--spadesMinKmerCovContigs N
Minimum contigs K-mer coverage. After assembly only
keep contigs with reported k-mer coverage equal or
above this value (default: 2)
SPAdes k-mers options (one of the following):
--spadesKmers 55 77 [55 77 ...]
Manually sets SPAdes k-mers lengths (all values must
be odd, lower than 128) (default values: reads
length >= 175 [55, 77, 99, 113, 127]; reads
length < 175 [21, 33, 55, 67, 77])
--spadesDefaultKmers Tells INNUca to use SPAdes default k-mers (default:
False)
Assembly Mapping options:
--assemblyMinCoverageContigs N
Minimum contigs average coverage. After mapping reads
back to the contigs, only keep contigs with at least
this average coverage (default: 1/3 of the assembly
mean coverage or 10x)
Assembly options:
--maxNumberContigs N Maximum number of contigs per 1.5 Mb of expected
genome size (default: 100)
--saveExcludedContigs Tells INNUca.py to save excluded contigs (default: False)
Pilon options:
--pilonKeepFiles Tells INNUca.py to not remove the output of Pilon
(default: False)
In order to combine INNUca reports (Estimate Coverage, True Coverage, Pear, SPAdes, Assembly Mapping, Pilon, MLST), use combine_reports.py found in INNUca modules folder
usage: python combine_reports.py [-h] [--version] -i
/path/to/INNUca/output/directory/
[-o /path/to/output/directory/]
Combine INNUca reports (Estimated Coverage, True Coverage, Pear, SPAdes, Assembly
Mapping, Pilon, MLST)
optional arguments:
-h, --help show this help message and exit
--version Version information
Required options:
-i /path/to/INNUca/output/directory/, --innucaOut /path/to/INNUca/output/directory/
Path to INNUca output directory (default: None)
Facultative options:
-o /path/to/output/directory/, --outdir /path/to/output/directory/
Path to where to store the outputs (default: ['.'])
In order to manually combine INNUca trueCoverage_ReMatCh module reports in respect to gene information, use combine_trueCoverage_reports.py found in INNUca modules/trueCoverage_rematch folder
usage: python combine_trueCoverage_reports.py [-h] [--version] -i
/path/to/INNUca/output/directory/
[-o /path/to/output/directory/]
[--minimum_gene_coverage 80]
Combine trueCoverage_ReMatCh module reports in respect to gene information.
optional arguments:
-h, --help show this help message and exit
--version Version information
Required options:
-i /path/to/INNUca/output/directory/, --innucaOut /path/to/INNUca/output/directory/
Path to INNUca output directory (default: None)
Facultative options:
-o /path/to/output/directory/, --outdir /path/to/output/directory/
Path to where to store the outputs (default: .)
--minimum_gene_coverage 80
Minimum percentage of sequence length (with a minimum
of read depth to consider a position to be present) to
determine whether a gene is present. (default: 80)
Miguel Machado mpmachado@medicina.ulisboa.pt
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