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
Installation
install with pip:
pip install notramp
install with conda:
conda create -n notramp
conda activate notramp
conda install -c simakro notramp
or
conda create -n notramp -c simakro notramp
conda activate notramp
Usage
USAGE:
install notramp package and run:
notramp (-a | -c | -t) -p PRIMERS -r READS -g REFERENCE [optional arguments]
or download source from github and run from package dir:
notramp_main.py (-a | -c | -t) -p PRIMERS -r READS -g REFERENCE [optional arguments]
All arguments in detail:
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.
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:
-h, --help Print help message and exit
-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 this flag if you want to include the primer sequences in the trimmed
reads. By default primers are removed together with all overhanging
sequences like barcodes and adapters.
-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]
-v, --version Print version and exit
Requirements/Dependencies
- Python 3.x
- minimap2
- psutil
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.