Liger2LiGer is a Nanopore chimera splitting/detection tool. Automated end-to-end chimera detection and dataset evaluation starting from fastq.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=4g -c4
[user@cn0911 ~]$module load liger2liger
[+] Loading singularity 3.10.5 on cn0911
[+] Loading liger2liger 20230901
[user@cn0911 ~]$evaluate_chimeras.py -h
usage: evaluate_chimeras.py [-h] --ref REF --fastq FASTQ [--dry] [--n_threads N_THREADS]
optional arguments:
-h, --help show this help message and exit
--ref REF, -r REF Path of reference fasta to use for alignment
--fastq FASTQ, -i FASTQ
comma-separated list of fastq file paths to be aligned
--dry echo the commands instead of executing them
--n_threads N_THREADS
How many threads to use for minimap2 alignment
[user@cn0911 ~]$extract_reads_from_fastq.py -h
usage: extract_reads_from_fastq.py [-h] --fastq FASTQ --ids IDS
optional arguments:
-h, --help show this help message and exit
--fastq FASTQ path of file containing FASTA/FASTQ sequence
--ids IDS path of file containing 1 id per line to be queried
[user@cn0911 ~]$filter_paf_by_read_name.py -h
usage: filter_paf_by_read_name.py [-h] --paf PAF --names NAMES
optional arguments:
-h, --help show this help message and exit
--paf PAF path of PAF file to be filtered
--names NAMES path of file containing a list of read ids, one on each line
[user@cn0911 ~]$generate_chimer_stats.py
usage: generate_chimer_stats.py [-h] --input INPUT [--output_dir OUTPUT_DIR] [--dry]
optional arguments:
-h, --help show this help message and exit
--input INPUT, -i INPUT
Comma separated paths of length txt files containing lengths of chimers and non-chimers (one length [in
bp] per line). Can run any number of pairs of txt files as long as they have the suffix
non_chimer_lengths.txt or chimer_lengths.txt and pairs share a prefix.
--output_dir OUTPUT_DIR, -o OUTPUT_DIR
Optionally create a directory to store the output.
--dry, -d Don't create any files, report output paths only.
Run liger2liger on sample data:
[user@cn0911 ~]$mkdir /data/$USER/L2L && cd /data/$USER/L2L [user@cn0911 ~]$cp $L2L_DATA/* . [user@cn0911 ~]$ln -s /fdb/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/Chromosomes/chrX.fa [user@cn0911 ~]$evaluate_chimeras.py --ref chrX.fa --fastq test.fastq --n_threads 2 STARTING: test_VS_chrX Found executable: /opt/conda/envs/l2l/Liger2LiGer/build/filter_chimeras_from_alignment minimap2 -x map-ont --secondary=no -n 10 -K 10g -k 17 -t 2 chrX.fa test.fastq [M::mm_idx_gen::0.863*1.00] collected minimizers [M::mm_idx_gen::1.122*1.23] sorted minimizers [M::main::1.122*1.23] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::1.197*1.22] mid_occ = 30 [M::mm_idx_stat] kmer size: 17; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::1.255*1.21] distinct minimizers: 3830080 (96.13% are singletons); average occurrences: 1.118; average spacing: 5.500 [M::worker_pipeline::1.276*1.21] mapped 350 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -x map-ont --secondary=no -n 10 -K 10g -k 17 -t 2 chrX.fa test.fastq [M::main] Real time: 1.286 sec; CPU: 1.551 sec; Peak RSS: 0.216 GB Writing chimeric reads to file: "/vf/users/user/L2L/test_VS_chrX/test_VS_chrX.chimeric_reads.txt" Writing non-chimeric reads to file: "/vf/users/user/L2L/test_VS_chrX/test_VS_chrX.non_chimeric_reads.txt" Writing chimeric lengths to file: "/vf/users/user/L2L/test_VS_chrX/test_VS_chrX.chimer_lengths.txt" Writing non-chimeric lengths to file: "/vf/users/user/L2L/test_VS_chrX/test_VS_chrX.non_chimer_lengths.txt" /vf/users/user/L2L/test_VS_chrX/test_VS_chrX.non_chimer_lengths.txt test_VS_chrX True True /vf/users/user/L2L/test_VS_chrX/test_VS_chrX.chimer_lengths.txt test_VS_chrX False True test N50 2625.0 Writing outputs to: /vf/users/user/L2L/test_VS_chrX/results_09_27_2023_09:03:52.csv Writing outputs to: results_09_27_2023_09:03:52.csv [user@cn0911 ~]$exitEnd the interactive session:
[user@cn0911 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$