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Andrea Telatin (QIB) committed Nov 5, 2021
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# dadaist2-rundada

```note
This is a new wrapper, introduced in 1.2.0, and experimental
```


```text
usage: dadaist2-rundada [-h] [-i INPUT_DIR] [-f FOR_DIR] [-r REV_DIR] -o OUTPUT_DIR [--tmp TMP] [--fortag FORTAG] [--revertag REVERTAG] [--sample-separator SAMPLE_SEPARATOR]
[--sample-extension SAMPLE_EXTENSION] [-q TRUNC_QUAL] [-j] [-p] [--trunc-len-1 TRUNC_LEN_1] [--trunc-len-2 TRUNC_LEN_2] [--trim-left-1 TRIM_LEFT_1] [--trim-left-2 TRIM_LEFT_2]
[--maxee-1 MAXEE_1] [--maxee-2 MAXEE_2] [--chimera {none,pooled,consensus}] [--min-parent-fold MIN_PARENT_FOLD] [--n-learn N_LEARN] [-t THREADS] [--keep-temp] [--log LOG] [--copy]
[--skip-checks] [--verbose]
Run DADA2
optional arguments:
-h, --help show this help message and exit
Main:
-i INPUT_DIR, --input-dir INPUT_DIR
Input directory with both R1 and R2
-f FOR_DIR, --for-dir FOR_DIR
Input directory with R1 reads
-r REV_DIR, --rev-dir REV_DIR
Input directory with R2 reads
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
Output directory
--tmp TMP Temporary directory
Input filtering:
--fortag FORTAG String defining a file as forward [default: _R1]
--revertag REVERTAG String defining a file as reverse [default: _R2]
--sample-separator SAMPLE_SEPARATOR
String acting as samplename separator [default: _]
--sample-extension SAMPLE_EXTENSION
String acting as samplename extension [default: .fastq.gz]
DADA2 parameters:
-q TRUNC_QUAL, --trunc-qual TRUNC_QUAL
Truncate at the first occurrence of a base with Q lower [default: 8]
-j, --join Join without merging
-p, --pool Pool samples
--trunc-len-1 TRUNC_LEN_1
Position at which to truncate forward reads [default: 0]
--trunc-len-2 TRUNC_LEN_2
Position at which to truncate reverse reads [default: 0]
--trim-left-1 TRIM_LEFT_1
Number of nucleotide to trim from the beginning of forward reads [default: 0]
--trim-left-2 TRIM_LEFT_2
Number of nucleotide to trim from the beginning of reverse reads [default: 0]
--maxee-1 MAXEE_1 Maximum expected errors in forward reads [default: 1.0]
--maxee-2 MAXEE_2 Maximum expected errors in reverse reads [default: 1.00]
--chimera {none,pooled,consensus}
Chimera handling can be none, pooled or consensus [default: pooled]
--min-parent-fold MIN_PARENT_FOLD
Minimum abundance of parents of a chimeric sequence (>1.0) [default: 1.0]
--n-learn N_LEARN Number of reads to learn the model, 0 for all [default: 0]
Other parameters:
-t THREADS, --threads THREADS
Number of threads
--keep-temp Keep temporary files
--log LOG Log file
--copy Copy input files instead of symbolic linking
--skip-checks Do not check installation of dependencies
--verbose Verbose mode
```

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