SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
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Download Latest Version (.zip)- 1_bug.yaml
- config.yml
- build-test-conda.yml
- check-conda-env.yml
- generate-docker-image.yml
- push-to-dockerhub-on-release.yml
- run-tests.yml
- 2025-4_Logos_AnaConesa_V3_SQANTI-lupa.png
- extra.css
- _Sidebar.md
- Dependencies-and-installation.md
- Home.md
- index.md
- Introduction-to-SQANTI3.md
- IsoAnnotLite.md
- Running-SQANTI-BUGSI.md
- Running-SQANTI-with-the-wrapper.md
- Running-SQANTI3-filter.md
- Running-SQANTI3-from-the-wrapper.md
- Running-SQANTI3-Quality-Control.md
- Running-SQANTI3-rescue-v5.1.md
- Running-SQANTI3-rescue.md
- Running-SQANTIโreads.md
- SQANTI3-memory-requeriments-and-paralellization.md
- Sqanti3-wrapper-script.md
- SQANTI3_isoform_classification.md
- Tusco-novel.md
- Tusco-quick-start.md
- Tutorial:-running-SQANTI3-on-an-example-dataset.md
- Understanding-the-output-of-SQANTI3-QC.md
- Version-history.md
- 2025-4_Logos_AnaConesa_V3_SQANTI3.png
- module_logger_config.json
- __init__.py
- BED.py
- BioReaders.py
- GFF.py
- SeqReaders.py
- __init__.py
- BED.py
- coordinate_mapper.py
- err_correct_w_genome.py
- sam_to_gff3.py
- STAR.py
- __init__.py
- compare_junctions.py
- filter_away_subset.py
- __init__.py
- LICENSE.md
- filter_default.json
- rules_filter_functions.py
- rules_filter_functions.R
- SQANTI3_MLfilter.R
- sqanti3_rules_filter.py
- SQANTI3_rules_filter.R
- compare_MLvariables.R
- SQANTI3_filter_report.R
- pigeon_generatePDFreport.R
- pigeon_report.R
- pigeon_report.Rmd
- data_prep_saturation.R
- LR_saturation.R
- plot_saturation.R
- generatePDFreport.R
- howToUse.png
- script.js
- SQANTI3_report.R
- SQANTI3_report.Rmd
- SQANTI3_TUSCO_Report.Rmd
- style.css
- tusco_human.tsv
- tusco_mouse.tsv
- TUSCO_report.R
- tusco_script.js
- tusco_style.css
- SQANTI3_rescue_report.R
- automatic_rescue.py
- automatic_rescue.R
- candidate_mapping_helpers.py
- old_requant_logic.py
- requant_helpers.py
- rescue_aux_functions.R
- rescue_by_mapping.py
- rescue_by_mapping_ML.R
- rescue_by_mapping_rules.py
- rescue_by_mapping_rules.R
- rescue_helpers.py
- run_randomforest_on_reference.R
- sq_requant.py
- gtfToGenePred-darwin-x86_64
- gtfToGenePred-linux-x86_64
- indels_annot.py
- IsoAnnotLite_SQ3.py
- rt_switching.py
- short_reads.py
- sqanti_reads_tables_and_plots_02ndk.py
- __init__.py
- argparse_utils.py
- classification__new.py
- classification_classifiers.py
- classification_main.py
- classification_preprocessing.py
- classification_steps.py
- classification_utils.py
- commands.py
- config.py
- filter_argparse.py
- filter_output.py
- filter_steps.py
- helpers.py
- logging_config.py
- module_logging.py
- parallel.py
- parsers.py
- qc_argparse.py
- qc_classes.py
- qc_computations.py
- qc_output.py
- qc_pipeline.py
- reads_argparse.py
- rescue_argparse.py
- rescue_output.py
- rescue_steps.py
- utils.py
- wrapper_utils.py
- write_parameters.py
- test_rules.py
- __init__.py
- test_tusco.py
- conftest.py
- conftest_requantification.py
- README_QC_TESTS.md
- README_REQUANTIFICATION_TESTS.md
- README_RESCUE_TESTS.md
- RESCUE_TESTS_QUICKSTART.md
- test_abundance.py
- test_classification.py
- test_junctions.py
- test_parallel.py
- test_qc_computations.py
- test_requantification.py
- test_rescue_automatic.py
- test_rescue_by_mapping.py
- test_rt_switching.py
- fl_count_empty.tsv
- fl_count_mixed_numeric.tsv
- fl_count_multi_sample.csv
- fl_count_multi_sample.tsv
- fl_count_single_sample.csv
- fl_count_single_sample.tsv
- fl_count_with_comments.tsv
- fl_count_with_na.tsv
- Rep1_test.bam
- Rep2_test.bam
- inside_TSS.bed
- mock_peaks.bed
- outside_TSS.bed
- genome.fasta
- genome_test.fasta
- junctions_temporal.txt
- inside_TSS.bed
- invalid_mock.renamed.fasta
- isoform_mock.fasta
- isoform_mock.fasta.gz
- isoform_mock.fasta.renamed.fasta
- isoform_mock.fastq
- isoforms.fasta
- outside_TSS.bed
- ratio_TSS.csv
- test_isoforms.fasta
- test_isoforms.fastq
- test_isoforms.genePred
- test_isoforms.gtf
- test_isoforms_classification.tsv
- sj.rts.results.tsv
- junctions_test.txt
- test_junctions.txt
- corrected_ORF_test.fasta
- TD2_test.faa
- chr_order.txt
- filter_rules.json
- ratio_TSS.csv
- refAnnotation_test.genePred
- test_reference.gtf
- test_reference.gtf_old
- automatic_rescue.tsv
- classification.tsv
- classification_lost_fsm.tsv
- classification_monoexon.tsv
- classification_multi_artifact.tsv
- classification_no_lost.tsv
- classification_rescue_automatic.tsv
- extended_classification.tsv
- mapping_hits.tsv
- reference_classification_filtered.tsv
- reference_mini.gtf
- reference_ml.tsv
- test_mapping.sam
- test_transcriptome.fasta
- sj.rts.results.tsv
- invalid_mock.renamed.fasta
- refAnnotation_test.genePred
- __init__.py
- README_RESCUE_BY_MAPPING_TESTS.md
- test_automatic_rescue.py
- test_candidate_mapping_helpers.py
- test_requant_helpers.py
- test_rescue_by_mapping_functions.py
- test_rescue_helpers.py
- test_rescue_output.py
- __init__.py
- test_rt_switching.py
- test_short_reads.py
- __init__.py
- test_classification_utils.py
- test_commands.py
- test_config.py
- test_filter_output.py
- test_helpers.py
- test_parsers.py
- test_qc_classes.py
- test_rules_filter_functions.py
- test_utils.py
- __init__.py
- old_test_argparser.py
- test_imports.py
- test_programs.py
- utils.py
- .gitignore
- .lintr
- build_docker.sh
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- Dockerfile
- LICENSE
- LICENSE.md
- Makefile
- mkdocs.yml
- pixi.lock
- pixi.toml
- pyproject.toml
- pytest.ini
- README.md
- setup.cfg
- sqanti3
- SQANTI3.conda_env.yml
- sqanti3_config.yaml
- sqanti3_filter.py
- sqanti3_qc.py
- sqanti3_reads.py
- sqanti3_rescue.py
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