Circularization-related utilities for the rotary pipeline
spokewrench, currently under development, is a suite of utilities for manipulating circular DNA elements. Once completed, these utilities will be able to serve as a modern replacement for circlator, which is now in a frozen development state. The utilities in spokewrench are built into the rotary project, where they are used with "best practices" to ensure proper assembly of circular sequences. These utilities can also be used in a standalone fashion or integrated into custom genome assembly workflows to ensure circular DNA/RNA elements are assembled accurately, similarly to how circlator is currently used.
git clone https://github.com/rotary-genomics/spokewrench.git
conda env create -n spokewrench --file=spokewrench/environment.yml
# Note: On Macs with Apple Silicon, you might need to add the flag '--platform osx-64' to force x64 install.
# The installed packages will then be converted to ARM architecture using Rosetta on first use.
conda activate spokewrench
cd spokewrench
pip install --editable .
# See available commands
spokewrench -hrepairRun on the outputs of Flye to repair the short gap or overlap region that can occur at the ends of circular contigs produced by this assembly tool.
Help menu (spokewrench repair -h):
usage: spokewrench repair [-h] [-lf PATH] [-O] [-v] -l PATH -a PATH -i PATH -o PATH [-f MODE] [-F FRACTION] [-I PERCENT] [-L LENGTH] [-e LENGTH] [-E LENGTH] [-k] [-c]
[-T LIST] [-t JOBS] [-m GB]
optional arguments:
-h, --help show this help message and exit
Basic config settings:
-lf PATH, --logfile PATH
Log filepath (default: None)
-O, --overwrite Overwrite existing files/directories. By setting this flag, you risk erasing old data.
-v, --verbose Enable verbose logging
Required:
-l PATH, --long_read_filepath PATH
QC-passing Nanopore reads
-a PATH, --assembly_fasta_filepath PATH
Contigs to be end-repaired
-i PATH, --assembly_info_filepath PATH
assembly_info.txt file from Flye showing which assembled contigs are circular vs. linear (or a custom guide file; see -c below)
-o PATH, --output_dir PATH
Output directory path
Input read options:
-f MODE, --flye_read_mode MODE
Type of long read reads provided by -l, to be used for reassembly by Flye. See details on these settings in the Flye documentation. (default: nano-hq)
-F FRACTION, --flye_read_error FRACTION
Expected error rate of input reads, expressed as proportion (e.g., 0.03). If "0", then have flye set the read error automatically (default: 0)
Merge options:
-I PERCENT, --circlator_min_id PERCENT
Percent identity threshold for circlator merge (default: 99)
-L LENGTH, --circlator_min_length LENGTH
Minimum required overlap (bp) between original and merge contigs (default: 10000)
-e LENGTH, --circlator_ref_end LENGTH
Minimum distance (bp) between end of original contig and nucmer hit (default: 100)
-E LENGTH, --circlator_reassemble_end LENGTH
Minimum distance (bp) between end of merge contig and nucmer hit (default: 100)
Workflow options:
-k, --keep_going_with_failed_contigs
Set this flag to continue running this script even if some contigs cannot be circularized and end-repaired. For any non-repaired contigs, an exact copy
of the original contig will be output.
-c, --custom_assembly_info_file
Set this flag if you provide a custom tab-separated file to specify the circular vs. linear status of each contig in the assembly, rather than using
the assembly_info.txt file output by Flye (default), as your argument to -i. The custom file must have the following format: no headers; tab-separated;
first column is the contig names; second column is the status of the contigs, either "circular" or "linear". Any contig names not in this file will be
dropped by the script!
-T LIST, --length_thresholds LIST
Comma-separated list of length thresholds for reassembly around the contig ends (bp) (default: 100000,75000,50000,25000,5000,2500,1000)
-t JOBS, --threads JOBS
Number of processors threads to use (default: 1)
-m GB, --threads_mem GB
Memory (GB) to use **per thread** for samtools sort (default: 1)rotateSupport module for rotating DNA sequences in FastA files.
Help menu (spokewrench rotate -h):
usage: spokewrench rotate [-h] [-lf PATH] [-O] [-v] -i PATH -o PATH [-m] [-p INT] [-P FLOAT] [-t PATH] [-T PATH] [-n LIST] [-r PATH] [-s]
optional arguments:
-h, --help show this help message and exit
Basic config settings:
-lf PATH, --logfile PATH
Log filepath (default: None)
-O, --overwrite Overwrite existing files/directories. By setting this flag, you risk erasing old data.
-v, --verbose Enable verbose logging
Required:
-i PATH, --input_fasta PATH
Input fasta file
-o PATH, --output_fasta PATH
Output fasta file. Note that all input sequences will always be written to output, even if only a subset of sequences are selected for rotate
operations.
Rotate options:
-m, --midpoint Rotate all sequences to their midpoint. (Incompatible with -p, -P, -t, and -T.)
-p INT, --rotate_position INT
Number of base positions to rotate all sequences by, in the counter-clockwise direction. To specify a unique rotate position for each sequence, see
-t). Incompatible with -m, -P, -t, and -T.
-P FLOAT, --rotate_fraction FLOAT
Fractional position to rotate all sequences to, counter-clockwise. For example, 0.3 means to rotate all contigs counter-clockwise to 30 percent of
their total length). To specify a unique fractional position for each sequence, see -T). Incompatible with -m, -p, -t, and -T.
-t PATH, --rotate_position_table PATH
Path to a tab-separated file that contains the desired amount to rotate each sequence by, in base pair position numbers, in the counter-clockwise
direction. Columns (with headers) should be "sequence_id" and "rotate_bp". Only sequences specified in the table will be rotated, although all
sequences in the input file will be written to the output file. Incompatible with -m, -p, -P, and -T.
-T PATH, --rotate_fraction_table PATH
Path to a tab-separated file that contains the desired amount to rotate each sequence by, as a fraction of total sequence length, in the counter-
clockwise direction. Columns (with headers) should be "sequence_id" and "rotate_fraction". Only sequences specified in the table will be rotated,
although all sequences in the input file will be written to the output file. Incompatible with -m, -p, -P, and -t.
-n LIST, --sequence_names LIST
Sequences to be rotated (comma-separated list of IDs). Rotate operations will only be applied to these sequences, although all sequences in the input
file will be written to output. If used with -t or -T, the sequences listed in the table will be further subset to those that are also in the provided
list of sequence names.
-r PATH, --output_report PATH
Path to write an optional tab-separated report file that shows how sequences were rotated.
Workflow options:
-s, --strip_descriptions
Strip descriptions off FastA headers (i.e., any text after the first whitespace in each header)