UDiTaS v1.1

Overview

UDiTaS(TM) stands for UniDirectional Targeted Sequencing, a novel sequencing method useful for measuring small indels as well as structural rearrangements, like translocations, in a single reaction.

See details of the method in Giannoukos et al. BMC Genomics (2018) 19:212, https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4561-9

Systems Requirements

UDiTaS has been tested in python 3.9 and requires the python packages and tools listed in the file uditas_env.yml

The code requires setting up two environmental variables

BOWTIE2_INDEXES contains the location of the bowtie2 index files, typically hg38.1.bt2, hg38.2.bt2, etc.

GENOMES_2BIT contains the location of the 2bit files for the genomes used in the analysis, eg hg38.2bit

To test the code create a virtual python environment with

conda env create -f uditas_env.yml

then activate using

source activate uditas_env

To install uditas as an executable run

python setup.py install

To test the installation run

pytest

This will process the test data in

data/fig2a
data/fig2b
data/fig2c

These data are subsamples of the data displayed in Fig 2 of the paper.

Usage

uditas is the main command to launch the UDiTaS analysis. The required argument is: dir_sample, the path of the directory with the data to be analyzed.

dir_sample should contain the fastq.gz files for R1, R2, I1 and I2. Used in the demultiplexing step.

dir_sample should also contain the analysis sheet sample_info.csv containing the description of all the samples, with their barcodes and guides used. See examples in the folder data

Once the setup has been run, the code can be run as

uditas ./data/fig2a

The full list of options are:

usage: uditas [-h] [-folder_genome_2bit FOLDER_GENOME_2BIT]
              [-skip_demultiplexing SKIP_DEMULTIPLEXING]
              [-skip_trimming SKIP_TRIMMING]
              [-skip_genome_local_alignment SKIP_GENOME_LOCAL_ALIGNMENT]
              [-skip_genome_global_alignment SKIP_GENOME_GLOBAL_ALIGNMENT]
              [-process_amplicon PROCESS_AMPLICON]
              [-skip_amplicon_global_alignment SKIP_AMPLICON_GLOBAL_ALIGNMENT]
              [-check_plasmid_insertions CHECK_PLASMID_INSERTIONS]
              [-skip_plasmid_alignment SKIP_PLASMID_ALIGNMENT] [-ncpu NCPU]
              [-window_size WINDOW_SIZE]
              [-default_amplicon_window_around_cut DEFAULT_AMPLICON_WINDOW_AROUND_CUT]
              [-min_MAPQ MIN_MAPQ] [-min_AS MIN_AS]
              [-process_AMP_seq_run PROCESS_AMP_SEQ_RUN]
              dir_sample

Process UDiTaS data

positional arguments:
  dir_sample            Directory with the sample to be processed

optional arguments:
  -h, --help            show this help message and exit
  -folder_genome_2bit FOLDER_GENOME_2BIT
                        Folder containing the 2bit file(s) with the reference
                        genome being used (default: GENOMES_2BIT)
  -skip_demultiplexing SKIP_DEMULTIPLEXING
                        Skip demultiplexing? Options: 0, 1 (skip) (default: 0)
  -skip_trimming SKIP_TRIMMING
                        Skip adapter trimming? Options: 0, 1 (skip) (default:
                        0)
  -skip_genome_local_alignment SKIP_GENOME_LOCAL_ALIGNMENT
                        Skip genome-wide local alignment? Options: 0 , 1
                        (skip) (default: 1)
  -skip_genome_global_alignment SKIP_GENOME_GLOBAL_ALIGNMENT
                        Skip genome-wide global alignment? Options: 0 , 1
                        (skip) (default: 0)
  -process_amplicon PROCESS_AMPLICON
                        Select row number (0-based) of amplicon to process,
                        set to all to process all amplicons (default: all)
  -skip_amplicon_global_alignment SKIP_AMPLICON_GLOBAL_ALIGNMENT
                        Skip amplicon global alignment? Options: 0, 1 (skip)
                        (default: 0)
  -check_plasmid_insertions CHECK_PLASMID_INSERTIONS
                        Check for plasmid insertions. Options: 0 (skip), 1
                        plamid_name and plasmid_sequence required in
                        sample_info.csv (default: 1)
  -skip_plasmid_alignment SKIP_PLASMID_ALIGNMENT
                        Skip plasmid alignment? Note, just alignment. Counts
                        still evaluated. Options: 0, 1 (skip) (default: 0)
  -ncpu NCPU            Number of CPUs to use (default: 4)
  -window_size WINDOW_SIZE
                        Window size around cut sites used to grab UDiTaS reads
                        (default: 15)
  -default_amplicon_window_around_cut DEFAULT_AMPLICON_WINDOW_AROUND_CUT
                        Window size around cut sites used to create amplicons
                        (default: 1000)
  -min_MAPQ MIN_MAPQ    Minimum mapping quality to include a read (default: 5)
  -min_AS MIN_AS        Minimum alignment score to include a read (default:
                        -180)
  -process_AMP_seq_run PROCESS_AMP_SEQ_RUN
                        Set to 1 to process an AMP-seq run using GUIDE-seq
                        adapters (default: 0)