Index

Symbols

--add_umi swibrid-demultiplex command line option --adjust_size swibrid-analyze_clustering command line option --aligned_seqs_path swibrid-combine_replicates command line option --aligner swibrid-combine_replicates command line option swibrid-downsample command line option --alignment_pars_path swibrid-combine_replicates command line option swibrid-downsample command line option --alignments swibrid-process_alignments command line option --annotation swibrid-create_bed command line option swibrid-plot_clustering command line option --bed swibrid-create_bed command line option swibrid-get_synthetic_reads command line option swibrid-get_unique_clones_bed command line option --bed_path swibrid-combine_replicates command line option swibrid-downsample command line option --big_clone_cutoff swibrid-downsample_clustering command line option swibrid-get_summary command line option --binsize swibrid-get_breakpoint_stats command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option --blacklist_regions swibrid-process_alignments command line option --blast swibrid-demultiplex command line option --breakpoint_alignments_path swibrid-combine_replicates command line option swibrid-downsample command line option --breakpoint_stats swibrid-get_summary command line option --chunksize swibrid-plot_clustering command line option --clean_column_names swibrid-collect_results command line option --cluster_analysis swibrid-get_summary command line option --cluster_analysis_path swibrid-collect_results command line option --cluster_downsampling swibrid-get_summary command line option --cluster_stats swibrid-collect_results command line option swibrid-downsample_clustering command line option swibrid-get_summary command line option --clustering swibrid-analyze_clustering command line option swibrid-find_variants command line option swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option swibrid-get_unique_clones_bed command line option --clustering_analysis swibrid-get_breakpoint_stats command line option --clustering_results swibrid-plot_clustering command line option --clustering_stats swibrid-plot_clustering command line option --cmax swibrid-plot_clustering command line option --collapse swibrid-demultiplex command line option --color_by swibrid-plot_clustering command line option --combined swibrid-combine_replicates command line option --config swibrid-run command line option swibrid-test command line option --coords swibrid-construct_msa command line option swibrid-plot_clustering command line option --cut swibrid-get_unique_clones_bed command line option --cutoff swibrid-demultiplex command line option swibrid-plot_clustering command line option --cutoff_color swibrid-plot_clustering command line option --dist swibrid-demultiplex command line option --distances swibrid-construct_linkage command line option --distribution swibrid-get_synthetic_reads command line option --dpi swibrid-plot_clustering command line option --fdr swibrid-find_variants command line option --fig_height swibrid-plot_clustering command line option --fig_width swibrid-plot_clustering command line option --figure swibrid-demultiplex command line option swibrid-get_summary command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-plot_clustering command line option swibrid-plot_demux_report command line option --filtering_cutoff swibrid-downsample_clustering command line option swibrid-find_clusters command line option --fit_method swibrid-find_clusters command line option --fix_cutoff swibrid-find_clusters command line option --gap_window_size swibrid-find_variants command line option --gaps swibrid-analyze_clustering command line option swibrid-construct_linkage command line option swibrid-downsample_clustering command line option swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option --genome swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-process_alignments command line option --haplotypes swibrid-find_variants command line option swibrid-plot_clustering command line option --help swibrid command line option swibrid-analyze_clustering command line option swibrid-collect_results command line option swibrid-combine_replicates command line option swibrid-construct_linkage command line option swibrid-construct_msa command line option swibrid-create_bed command line option swibrid-demultiplex command line option swibrid-downsample command line option swibrid-downsample_clustering command line option swibrid-find_clusters command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_alignment_pars command line option swibrid-get_annotation command line option swibrid-get_breakpoint_stats command line option swibrid-get_gaps command line option swibrid-get_summary command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-get_synthetic_reads command line option swibrid-get_unique_clones_bed command line option swibrid-plot_clustering command line option swibrid-plot_demux_report command line option swibrid-process_alignments command line option swibrid-run command line option swibrid-setup command line option swibrid-test command line option --homology swibrid-get_breakpoint_stats command line option --ignore_order swibrid-process_alignments command line option --ignore_unused_positions swibrid-construct_linkage command line option swibrid-downsample_clustering command line option --inf swibrid-get_alignment_pars command line option --info swibrid-get_summary command line option swibrid-get_synthetic_reads command line option swibrid-plot_clustering command line option swibrid-process_alignments command line option --info_path swibrid-combine_replicates command line option swibrid-downsample command line option --input swibrid-demultiplex command line option swibrid-downsample command line option swibrid-find_clusters command line option swibrid-get_annotation command line option --inserts swibrid-analyze_clustering command line option swibrid-collect_results command line option --inserts_path swibrid-collect_results command line option --inserts_tsv_path swibrid-combine_replicates command line option swibrid-downsample command line option --interrupt_for_read swibrid-process_alignments command line option --isotype_extra swibrid-analyze_clustering command line option swibrid-process_alignments command line option --k swibrid-get_synthetic_reads command line option --keep_internal swibrid-process_alignments command line option --keep_secondary_alignments swibrid-process_alignments command line option --linkage swibrid-construct_linkage command line option swibrid-find_clusters command line option swibrid-plot_clustering command line option --linkage_border swibrid-plot_clustering command line option --mat swibrid-find_rearrangements command line option swibrid-find_variants command line option --max_gap swibrid-analyze_clustering command line option swibrid-construct_linkage command line option swibrid-downsample_clustering command line option swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option swibrid-process_alignments command line option --max_insert_gap swibrid-process_alignments command line option --max_insert_overlap swibrid-process_alignments command line option --max_local_gap_freq swibrid-find_variants command line option --max_n_blunt swibrid-get_summary command line option --max_realignment_gap swibrid-analyze_clustering command line option --max_rearrangement_gap swibrid-find_rearrangements command line option --max_split_dist swibrid-demultiplex command line option --max_switch_overlap swibrid-process_alignments command line option --method swibrid-construct_linkage command line option swibrid-downsample_clustering command line option --metric swibrid-construct_linkage command line option swibrid-downsample_clustering command line option --min_cluster_cov swibrid-find_variants command line option --min_cov swibrid-find_variants command line option swibrid-process_alignments command line option --min_freq swibrid-find_variants command line option --min_insert_match swibrid-process_alignments command line option --min_length swibrid-process_alignments command line option --min_num_switch_matches swibrid-process_alignments command line option --min_reads swibrid-demultiplex command line option --min_switch_match swibrid-process_alignments command line option --min_telo_matchlen swibrid-process_alignments command line option --motifs swibrid-find_variants command line option swibrid-get_breakpoint_stats command line option swibrid-get_switch_motifs command line option --msa swibrid-analyze_clustering command line option swibrid-construct_linkage command line option swibrid-construct_msa command line option swibrid-downsample_clustering command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_gaps command line option swibrid-plot_clustering command line option --msa_csv swibrid-get_gaps command line option --msa_csv_path swibrid-combine_replicates command line option swibrid-downsample command line option --msa_path swibrid-combine_replicates command line option swibrid-downsample command line option --n swibrid-downsample command line option swibrid-get_synthetic_reads command line option --n_backup swibrid-construct_linkage command line option --n_neighbors swibrid-construct_linkage command line option --n_threads swibrid-construct_linkage command line option --nbinom_alpha swibrid-get_synthetic_reads command line option --nmax swibrid-combine_replicates command line option swibrid-construct_linkage command line option swibrid-construct_msa command line option swibrid-demultiplex command line option --no_deletions swibrid-get_synthetic_reads command line option --no_insertions swibrid-get_synthetic_reads command line option --no_mutations swibrid-get_synthetic_reads command line option --no_x_ticks swibrid-plot_clustering command line option --nreads swibrid-downsample_clustering command line option swibrid-find_variants command line option --nreps swibrid-downsample_clustering command line option

--ntop swibrid-get_breakpoint_stats command line option --omit_scale_bar swibrid-plot_clustering command line option --only_complete swibrid-process_alignments command line option --out swibrid-construct_msa command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_alignment_pars command line option swibrid-get_annotation command line option swibrid-get_breakpoint_stats command line option swibrid-get_gaps command line option swibrid-get_synthetic_reads command line option --outdir swibrid-demultiplex command line option swibrid-plot_demux_report command line option --outfile swibrid-create_bed command line option swibrid-process_alignments command line option --output swibrid-analyze_clustering command line option swibrid-downsample command line option swibrid-find_clusters command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-get_unique_clones_bed command line option --overwrite swibrid-setup command line option swibrid-test command line option --paired_end_mode swibrid-create_bed command line option swibrid-get_gaps command line option swibrid-plot_clustering command line option swibrid-process_alignments command line option --par swibrid-get_synthetic_reads command line option --pars swibrid-find_variants command line option --plot swibrid-get_breakpoint_stats command line option --process swibrid-get_summary command line option --process_path swibrid-combine_replicates command line option swibrid-downsample command line option --process_stats_path swibrid-combine_replicates command line option swibrid-downsample command line option --processed_alignments swibrid-create_bed command line option --queue swibrid-run command line option swibrid-test command line option --range swibrid-get_breakpoint_stats command line option swibrid-get_switch_homology command line option --raw_reads swibrid-create_bed command line option swibrid-process_alignments command line option --realign_breakpoints swibrid-process_alignments command line option --realignment_penalties swibrid-process_alignments command line option --realignments swibrid-analyze_clustering command line option swibrid-plot_clustering command line option --rearrangements swibrid-get_breakpoint_stats command line option swibrid-get_synthetic_reads command line option --ref swibrid-get_alignment_pars command line option --reference swibrid-find_variants command line option swibrid-get_breakpoint_stats command line option swibrid-get_synthetic_reads command line option --remove_duplicates swibrid-process_alignments command line option --remove_isotypes swibrid-process_alignments command line option --report swibrid-demultiplex command line option --sample swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option swibrid-plot_clustering command line option --sample_sheet swibrid-demultiplex command line option swibrid-plot_demux_report command line option --sample_stats swibrid-collect_results command line option --samples swibrid-collect_results command line option swibrid-combine_replicates command line option --save_all swibrid-find_variants command line option --scale_factor swibrid-get_breakpoint_stats command line option --scanning swibrid-find_clusters command line option swibrid-get_summary command line option --seed swibrid-get_synthetic_reads command line option --sequences swibrid-construct_msa command line option swibrid-process_alignments command line option --sge swibrid-run command line option swibrid-test command line option --show_inserts swibrid-plot_clustering command line option --sidebar_color_by swibrid-plot_clustering command line option --slurm swibrid-run command line option swibrid-test command line option --snakefile swibrid-run command line option swibrid-test command line option --split_reads swibrid-demultiplex command line option --stats swibrid-downsample_clustering command line option swibrid-find_clusters command line option swibrid-find_variants command line option swibrid-get_summary command line option swibrid-process_alignments command line option --summary_path swibrid-collect_results command line option --switch_annotation swibrid-analyze_clustering command line option swibrid-construct_msa command line option swibrid-create_bed command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-plot_clustering command line option swibrid-process_alignments command line option --switch_coords swibrid-analyze_clustering command line option swibrid-construct_msa command line option swibrid-create_bed command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-plot_clustering command line option swibrid-process_alignments command line option --telo swibrid-process_alignments command line option --telo_cutoff swibrid-process_alignments command line option --top_acceptor swibrid-get_breakpoint_stats command line option --top_donor swibrid-get_breakpoint_stats command line option --umi_regex swibrid-demultiplex command line option --use_clones swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option --use_orientation swibrid-construct_msa command line option --use_sparse swibrid-construct_linkage command line option --variant_annotation swibrid-find_variants command line option --variants swibrid-get_summary command line option swibrid-get_synthetic_reads command line option --variants_matrix swibrid-plot_clustering command line option --variants_table swibrid-plot_clustering command line option --verbose swibrid command line option --version swibrid command line option --weights swibrid-get_breakpoint_stats command line option swibrid-get_summary command line option --write_info_chunks swibrid-demultiplex command line option -a swibrid-get_breakpoint_stats command line option -b swibrid-demultiplex command line option swibrid-get_breakpoint_stats command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-get_synthetic_reads command line option swibrid-get_unique_clones_bed command line option -C swibrid-find_clusters command line option -c swibrid-combine_replicates command line option swibrid-demultiplex command line option swibrid-find_clusters command line option swibrid-get_breakpoint_stats command line option swibrid-get_unique_clones_bed command line option swibrid-run command line option swibrid-test command line option -d swibrid-demultiplex command line option swibrid-get_synthetic_reads command line option -f swibrid-demultiplex command line option swibrid-find_clusters command line option swibrid-plot_demux_report command line option swibrid-setup command line option swibrid-test command line option -g swibrid-get_breakpoint_stats command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option -h swibrid command line option swibrid-analyze_clustering command line option swibrid-collect_results command line option swibrid-combine_replicates command line option swibrid-construct_linkage command line option swibrid-construct_msa command line option swibrid-create_bed command line option swibrid-demultiplex command line option swibrid-downsample command line option swibrid-downsample_clustering command line option swibrid-find_clusters command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_alignment_pars command line option swibrid-get_annotation command line option swibrid-get_breakpoint_stats command line option swibrid-get_gaps command line option swibrid-get_summary command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-get_synthetic_reads command line option swibrid-get_unique_clones_bed command line option swibrid-plot_clustering command line option swibrid-plot_demux_report command line option swibrid-process_alignments command line option swibrid-run command line option swibrid-setup command line option swibrid-test command line option -i swibrid-demultiplex command line option swibrid-downsample command line option swibrid-find_clusters command line option swibrid-get_alignment_pars command line option swibrid-get_annotation command line option swibrid-get_synthetic_reads command line option -k swibrid-get_switch_motifs command line option swibrid-get_synthetic_reads command line option -l swibrid-find_clusters command line option -m swibrid-demultiplex command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option -n swibrid-downsample command line option swibrid-find_clusters command line option swibrid-get_breakpoint_stats command line option swibrid-get_synthetic_reads command line option -o swibrid-analyze_clustering command line option swibrid-demultiplex command line option swibrid-downsample command line option swibrid-find_clusters command line option swibrid-find_rearrangements command line option swibrid-find_variants command line option swibrid-get_alignment_pars command line option swibrid-get_annotation command line option swibrid-get_breakpoint_stats command line option swibrid-get_gaps command line option swibrid-get_switch_homology command line option swibrid-get_switch_motifs command line option swibrid-get_synthetic_reads command line option swibrid-get_unique_clones_bed command line option swibrid-plot_demux_report command line option -p swibrid-get_breakpoint_stats command line option swibrid-get_synthetic_reads command line option -r swibrid-demultiplex command line option swibrid-get_alignment_pars command line option swibrid-get_breakpoint_stats command line option swibrid-get_synthetic_reads command line option -s swibrid-combine_replicates command line option swibrid-demultiplex command line option swibrid-downsample_clustering command line option swibrid-find_clusters command line option swibrid-get_synthetic_reads command line option swibrid-plot_demux_report command line option swibrid-run command line option swibrid-test command line option -v swibrid command line option

S

snake_options swibrid-run command line option swibrid-test command line option swibrid command line option --help --verbose --version -h -v swibrid-analyze_clustering command line option --adjust_size --clustering --gaps --help --inserts --isotype_extra --max_gap --max_realignment_gap --msa --output --realignments --switch_annotation --switch_coords -h -o swibrid-collect_results command line option --clean_column_names --cluster_analysis_path --cluster_stats --help --inserts --inserts_path --sample_stats --samples --summary_path -h swibrid-combine_replicates command line option --aligned_seqs_path --aligner --alignment_pars_path --bed_path --breakpoint_alignments_path --combined --help --info_path --inserts_tsv_path --msa_csv_path --msa_path --nmax --process_path --process_stats_path --samples -c -h -s swibrid-construct_linkage command line option --distances --gaps --help --ignore_unused_positions --linkage --max_gap --method --metric --msa --n_backup --n_neighbors --n_threads --nmax --use_sparse -h swibrid-construct_msa command line option --coords --help --msa --nmax --out --sequences --switch_annotation --switch_coords --use_orientation -h swibrid-create_bed command line option --annotation --bed --help --outfile --paired_end_mode --processed_alignments --raw_reads --switch_annotation --switch_coords -h swibrid-demultiplex command line option --add_umi --blast --collapse --cutoff --dist --figure --help --input --max_split_dist --min_reads --nmax --outdir --report --sample_sheet --split_reads --umi_regex --write_info_chunks -b -c -d -f -h -i -m -o -r -s swibrid-downsample command line option --aligner --alignment_pars_path --bed_path --breakpoint_alignments_path --help --info_path --input --inserts_tsv_path --msa_csv_path --msa_path --n --output --process_path --process_stats_path -h -i -n -o swibrid-downsample_clustering command line option --big_clone_cutoff --cluster_stats --filtering_cutoff --gaps --help --ignore_unused_positions --max_gap --method --metric --msa --nreads --nreps --stats -h -s swibrid-find_clusters command line option --filtering_cutoff --fit_method --fix_cutoff --help --input --linkage --output --scanning --stats -c -C -f -h -i -l -n -o -s swibrid-find_rearrangements command line option --help --mat --max_rearrangement_gap --msa --out --switch_annotation --switch_coords -h -m -o swibrid-find_variants command line option --clustering --fdr --gap_window_size --haplotypes --help --mat --max_local_gap_freq --min_cluster_cov --min_cov --min_freq --motifs --msa --nreads --out --pars --reference --save_all --stats --switch_annotation --switch_coords --variant_annotation -h -m -o swibrid-get_alignment_pars command line option --help --inf --out --ref -h -i -o -r swibrid-get_annotation command line option --help --input --out -h -i -o swibrid-get_breakpoint_stats command line option --binsize --clustering --clustering_analysis --gaps --help --homology --max_gap --motifs --ntop --out --plot --range --rearrangements --reference --sample --scale_factor --switch_annotation --switch_coords --top_acceptor --top_donor --use_clones --weights -a -b -c -g -h -n -o -p -r

swibrid-get_gaps command line option --help --msa --msa_csv --out --paired_end_mode -h -o swibrid-get_summary command line option --big_clone_cutoff --breakpoint_stats --cluster_analysis --cluster_downsampling --cluster_stats --clustering --figure --gaps --help --info --max_gap --max_n_blunt --process --sample --scanning --stats --switch_annotation --switch_coords --use_clones --variants --weights -h swibrid-get_switch_homology command line option --binsize --figure --genome --help --output --range --switch_annotation --switch_coords -b -g -h -o swibrid-get_switch_motifs command line option --binsize --figure --genome --help --motifs --output --switch_annotation --switch_coords -b -g -h -k -o swibrid-get_synthetic_reads command line option --bed --distribution --help --info --k --n --nbinom_alpha --no_deletions --no_insertions --no_mutations --out --par --rearrangements --reference --seed --variants -b -d -h -i -k -n -o -p -r -s swibrid-get_unique_clones_bed command line option --bed --clustering --cut --help --output -b -c -h -o swibrid-plot_clustering command line option --annotation --chunksize --clustering_results --clustering_stats --cmax --color_by --coords --cutoff --cutoff_color --dpi --fig_height --fig_width --figure --haplotypes --help --info --linkage --linkage_border --msa --no_x_ticks --omit_scale_bar --paired_end_mode --realignments --sample --show_inserts --sidebar_color_by --switch_annotation --switch_coords --variants_matrix --variants_table -h swibrid-plot_demux_report command line option --figure --help --outdir --sample_sheet -f -h -o -s swibrid-process_alignments command line option --alignments --blacklist_regions --genome --help --ignore_order --info --interrupt_for_read --isotype_extra --keep_internal --keep_secondary_alignments --max_gap --max_insert_gap --max_insert_overlap --max_switch_overlap --min_cov --min_insert_match --min_length --min_num_switch_matches --min_switch_match --min_telo_matchlen --only_complete --outfile --paired_end_mode --raw_reads --realign_breakpoints --realignment_penalties --remove_duplicates --remove_isotypes --sequences --stats --switch_annotation --switch_coords --telo --telo_cutoff -h swibrid-run command line option --config --help --queue --sge --slurm --snakefile -c -h -s snake_options swibrid-setup command line option --help --overwrite -f -h swibrid-test command line option --config --help --overwrite --queue --sge --slurm --snakefile -c -f -h -s snake_options