zymoresearch/pfind repository overview

Launch EC2 instance and run dropout_pipeline for project.

positional arguments:
  project_name      Targeted sequencing project name. eg. zr1172

optional arguments:
  -h, --help        show this help message and exit
  -t INSTANCE_TYPE  EC2 instance type. (Default: r3.2xlarge)

Execute dropout_heatmap, dropout_bamfiles and dropout_barcharts in pipeline.

positional arguments:
  project_name          Targeted sequencing project name. eg. zr1172

optional arguments:
  -h, --help            show this help message and exit
  --cutoff CUTOFF       [HEATMAP]The minimum number of reads required for an
                        valid amplicon. (Default: 10)
  --read-pos-shift READ_POS_SHIFT
                        [HEATMAP]The maximum position shift allowed between
                        amplicon start/end coordinates and actual read
                        start/end coordinates. (Default: 0)
  --primer-cutoff PRIMER_CUTOFF
                        [BAMFILES]The maximum number of mismatches and gaps
                        allowed in the first 20 base pairs of a sequencing
                        read. (Default: 3)
  --score-cutoff SCORE_CUTOFF
                        [BAMFILES]The minimum score per base pair that a
                        read/amplicon pairwise alignment should have.
                        (Default: 4 out of 5)
  --bam-dir BAM_DIR     [BARCHARTS]The directory where the bam files of
                        unmapped reads are. (Default: /mnt/dropout_bamfiles)
  -l {full,pre_barcharts,post_heatmap,heatmap,bamfiles,barcharts}
                        Select level of executing pipeline scripts. (Default:
                        full)
  -u                    Toggle S3 upload.
  -o OUT_DIR            The output directory. (Default: /mnt)

Draw heatmap to visualize mapped reads distribution among all samples and
amplicons.

positional arguments:
  project_name       Targeted sequencing project name. eg. zr1172

optional arguments:
  -h, --help         show this help message and exit
  -c CUTOFF          The minimum number of reads required for an valid
                     amplicon. (Default: 10)
  -t READ_POS_SHIFT  The maximum position shift allowed between amplicon
                     start/end coordinates and actual read start/end
                     coordinates. (Default: 0)
  -u                 Toggle S3 upload.
  -o OUT_DIR         The output directory. (Default: /mnt)

Perform analysis and create bam files for the unmapped reads across samples.

positional arguments:
  project_name      Targeted sequencing project name. eg. zr1172

optional arguments:
  -h, --help        show this help message and exit
  -p PRIMER_CUTOFF  The maximum number of mismatches and gaps allowed in the
                    first 20 base pairs of a sequencing read. (Default: 3)
  -c SCORE_CUTOFF   The minimum score per base pair that a read/amplicon
                    pairwise alignment should have. (Default: 4 out of 5)
  -u                Toggle S3 upload.
  -o OUT_DIR        The output directory. (Default: /mnt)

Draw stacked bar charts for each amplicon to visualize issues that cause
dropout.

positional arguments:
  project_name  Targeted sequencing project name. eg. zr1172

optional arguments:
  -h, --help    show this help message and exit
  -b BAM_DIR    The directory where the bam files of unmapped reads are.
                (Default: /mnt/dropout_bamfiles)
  -u            Toggle S3 upload.
  -o OUT_DIR    The output directory. (Default: /mnt)