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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
+```