.. _flags-page:
Flags
=====
Required flags
--------------
| **Datastructure flags**
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* - Flag
- Input type
- Description
* - --db
- PATH
- The **directory** containing the preindexed :file:`Kraken` or :file:`KrakenUniq` database (see: :ref:`quicksand_build-page`)::
Input:
refseq
├── kraken
│ └── Mito_db_kmer22
│ ├── taxonomy
│ ├── ...
│ └── database.kdb
Example:
--db Path/to/refseq/kraken/Mito_db_kmer22
* - --genomes
- PATH
- | The **directory** containing the indexed FASTA-FILES of the reference genomes that were used to build
| the kraken database. Format :file:`PATH/$\\{family\\}/$\\{species\\}.fasta` (see: :ref:`quicksand_build-page`)
::
Input:
refseq
├── genomes
│ └── Hominidae
│ ├── Homo_sapiens.fasta
│ └── ...
Example:
--genomes Path/to/refseq/genomes
* - --bedfiles
- PATH
- | The **directory** containing the dustmasked BED-FILES of the reference genomes FASTA-FILES
| Format :file:`DIR/$\\{species\\}_masked.bed` (see: :ref:`quicksand_build-page`)
::
Input:
refseq
├── masked
│ ├── Homo_sapiens_masked.bed
│ └── ...
Example:
--bedfiles Path/to/refseq/masked
| **Input flags**
quicksand contains an optional demultiplexing preprocessing. However, it is an inhouse demultiplexer working only on bam-files
provided by the `MPI EVA Core Unit `_. For the processing of data coming from the
MPI EVA run quicksand with the :code:`--bam PATH` and :code:`--rg PATH` flags as alternative to the :code:`--split PATH` parameter.
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* - Flag
- Input type
- Description
* - --split
- PATH
- | Standard input
| A **directory** containing the demultiplexed, adapter trimmed (and overlap-merged) input files
::
Input:
split
├── RG1.bam
├── RG2.fastq
├── RG3.fastq.gz
├── RG4.fq.gz
└── ...
Example:
--split Path/to/split/
* - --bam
- PATH
- | Use together with the :code:`--rg` flag
| The multiplexed BAM-FILE, as provided by the `MPI EVA Core Unit `_ containing
| adapter-trimmed and overlap-merged sequencing reads
::
Example:
--bam Path/to/input.bam
* - --rg
- PATH
- | Use together with the :code:`--bam` flag
| A TSV-FILE, containing library information for the demultiplexing step.
| Provide the readgroups and respective primer combinations contained in the BAM FILE
::
Input (index.tsv):
#Index library ID primer_P7 primer_P5
RG1 1113 1137
RG2 1114 1138
Example:
--rg Path/to/index.tsv
Optional flags
--------------
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* - Flag
- Input type
- Description
* - --fixed
- PATH
- | Provide a TSV file
| Map :file:`extractedReads` to the specified genome for given families instead of the one determinded by quicksand.
| The tag is used as 'Species' name in the reports and the filenames.
::
Input (fixed.tsv):
Family Species(tag) Genome
Hominidae Homo_sapiens /path/to/seq.fa
Example:
--fixed Path/to/fixed.tsv
* - --rerun
- -
- | Run the pipeline in an already processed folder
| Works together with the :code:`--fixed` flag
| Map already extracted reads of families or orders to all the species assigned in the
| :code:`--fixed` references file.
| These records are **added** to the final_report file
::
Example:
--fixed Path/to/fixed.tsv --rerun
* - --taxlvl
- [o,f]
- | Default: f
| Change taxon level (family or order level) of binned sequences after KrakenUniq.
| Binned reads are still mapped against the genomes of each `families` reference genome.
|
| Example: Map all reads assigned to Primates to the Homo_sapiens genome
| **Note:** For the order-level bins, Binned reads are mapped several times to different (family) genomes.
::
Example:
--taxlvl o
* - --doublestranded
-
- | Count C to T at the 5' and G to A substitutions at the 3' end of mapped sequences,
| Default: Count C to T substitutions on 5' and 3' ends.
::
Example:
--doublestranded
**Process parameters**
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* - Flag
- Input type
- Description
* - --bamfilterflag
- N
- | For initial bam file filtering
| Filter the file based on the provided SAMTOOLS FLAG (default: 1 = filter paired reads).
| see `HERE `_ to find a desired filterflag
::
Example:
--bamfilterflag 5
* - --bamfilter_length_cutoff
- N
- | For initial bam file filtering
| Filter out reads below the given length cutoff (default: 35).
::
Example:
--bamfilter_length_cutoff 35
* - --krakenuniq_min_kmers
- N
- | For metagenomic classification
| Remove families from the KrakenUniq classification results with a kmer-count of less than N (default: 129).
::
Example:
--krakenuniq_min_kmers 129
* - --krakenuniq_min_reads
- N
- | For metagenomic classification
| Remove families from the KrakenUniq classification results with less than N reads assigned (default: 3).
::
Example:
--krakenuniq_min_reads 3
* - --bamfilter_quality_cutoff
- N
- | For after the mapping step
| Filter out reads with a mapping quality below the given quality cutoff (default: 25).
::
Example:
--bamfilter_quality_cutoff 25
* - --reportfilter_percentage
- N
- | For the creation of the filtered_report.tsv file
| Filter family assignments from the final_report.tsv that have a FamPercentage value of less or equal than N percent (default: 0.5).
::
Example:
--reportfilter_percentage 0.5
* - --reportfilter_breadth
- N
- | For the creation of the filtered_report.tsv file
| Filter family assignments from the final_report.tsv that have a ProportionExpectedBreadth value of less or equal than N (default: 0.5).
::
Example:
--reportfilter_breadth 0.8
* - --compression_level
- [0-9]
- | For the BAM output processes
| Set BGZF compression level (default: 0)
::
Example:
--compression_level 9
Profiles
--------
| Quicksand includes several profiles that can be used with the :code:`-profile` flag (Be aware: only one dash -)
| delimit multiple profiles by comma
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* - Profile
- Description
* - singularity
- Use Singularity as container software
* - docker
- Use Docker as container software
* - debug
- Keep intermediate files in the :file:`work` directory