Normalization and Trimming of long-read (ONT, PB) amplicon sequencing data
Project description
NoTrAmp
Normalization and Trimming of long-read (ONT, PB) amplicon sequencing data
NoTrAmp is a Tool for read-depth normalization and trimming of amplicon reads generated with long read technologies (ONT/PacBio). It can be used in amplicon-tiling approaches to cap coverage of each amplicon and to trim amplicons to their appropriate length removing barcodes, adpaters and primers (if desired) in a single clipping step.
Table of Contents
Commmand line Options
usage: notramp.py [-h] -p PRIMERS -r READS -g REFERENCE (-a | -c | -t) [-o OUT_DIR] [-m MAX_COV] [--incl_prim] [-s SEQ_TEC] [-n NAME_SCHEME] [--set_min_len SET_MIN_LEN] [--set_max_len SET_MAX_LEN]
[--set_margins MARGINS]
NoTrAmp is a Tool for read-depth normalization and trimming of amplicon reads generated with long read technologies (ONT/PacBio). It can be used in amplicon-tiling approaches to cap coverage of each
amplicon and to trim amplicons to their appropriate length removing barcodes, adpaters and primers (if desired) in a single clipping step.
optional arguments:
-h, --help show this help message and exit
Required arguments:
-p PRIMERS, --primers PRIMERS
Path to primer bed-file (primer-names must adhere to a consistent naming scheme see readme)
-r READS, --reads READS
Path to sequencing reads fasta
-g REFERENCE, --reference REFERENCE
Path to reference (genome)
-a, --all Perform read depth normalization by coverage-capping/downsampling first, then clip the normalized reads. (mut.excl. with -c, -t)
-c, --cov Perform only read-depth normalization/downsampling. (mut.excl. with -a, -t)
-t, --trim Perform only trimming to amplicon length (excluding primers by default; to include primers set --incl_prim flag). (mut.excl. with -a, -c)
Optional arguments:
-o OUT_DIR Optionally specify a directory for saving of outfiles. If this argument is not given, out-files will be saved in the directory where the input reads are located. [default=False]
-m MAX_COV Provide threshold for maximum read-depth per amplicon as integer value. [default=200]
--incl_prim Set to False if you want to include the primer sequences in the trimmed reads. By default primers are removed together with all overhanging sequences. [default=False]
-s SEQ_TEC Specify long-read sequencing technology (ont/pb). [default='ont']
-n NAME_SCHEME Provide path to json-file containing a naming scheme which is consistently used for all primers. [default='artic_nCoV_scheme']
--set_min_len SET_MIN_LEN
Set a minimum required length for alignments of reads to amplicon. If this is not set the min_len will be 0.5*average_amp_len. If amplicon sizes are relatively homogenous this
parameter is not required [default=False]
--set_max_len SET_MAX_LEN
Set a maximum required length for alignments of reads to amplicon. If this is not set the max_len will be 1.5*average_amp_len. If amplicon sizes are relatively homogenous this
parameter is not required [default=False]
--set_margins MARGINS
Set length of tolerance margins for sorting of mappings to amplicons. [default=5]
## <a name="depend"></a>Requirements/Dependencies
- Python 3.x
- minimap2
- psutil
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