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packages"],"sub_categories":["Transcriptomics"],"readme":"[![BioConda Install](https://img.shields.io/conda/dn/bioconda/isoquant.svg?style=flag\u0026label=BioConda%20install)](https://anaconda.org/bioconda/isoquant)\n[![PyPI Downloads](https://img.shields.io/pypi/v/isoquant)](https://pypi.org/project/isoquant/)\n[![Python version](https://img.shields.io/badge/python-3.8-blue)](https://www.python.org/downloads/)\n[![License](https://img.shields.io/badge/licence-GPLv2-blue)](https://www.gnu.org/licenses/old-licenses/gpl-2.0)\n[![GitHub release (latest by date)](https://img.shields.io/github/v/release/ablab/IsoQuant)](https://github.com/ablab/IsoQuant/releases/)\n[![GitHub Downloads](https://img.shields.io/github/downloads/ablab/IsoQuant/total.svg?style=social\u0026logo=github\u0026label=Download)](https://github.com/ablab/IsoQuant/releases)\n[![UnitTests](https://github.com/ablab/IsoQuant/actions/workflows/Unit_tests.yml/badge.svg)](https://github.com/ablab/IsoQuant/actions/workflows/Unit_tests.yml)\n[![User manual](https://github.com/ablab/IsoQuant/actions/workflows/docs.yml/badge.svg)](https://ablab.github.io/IsoQuant/)\n\n\n\u003cimg src=\"https://raw.githubusercontent.com/ablab/IsoQuant/master/docs/isoquant_logo.png\" width=\"300\" alt=\"IsoQuant\"\u003e\n\n[Full IsoQuant documentation can be found here](https://ablab.github.io/IsoQuant/).\nInformation in this README is given only for convenience and is not a full user manual.\n\nCurrent version: see `VERSION` file.\n\n* [Citation information](#citation)\n* [Feedback and bug reports](#feedback-and-bug-reports)\n* [Quick start examples](#quick-start)\n\n\n## About IsoQuant\n\nIsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or\nOxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with\nhigh precision and decent recall. If the reference annotation is given, IsoQuant also\nassigns reads to the annotated isoforms based on their intron and exon structure.\nIsoQuant further performs annotated gene, isoform, exon, and intron quantification.\nIf reads are grouped (e.g. according to a cell type), counts are reported according to the provided grouping.\n\nThe latest IsoQuant version can be downloaded from [github.com/ablab/IsoQuant/releases/latest](https://github.com/ablab/IsoQuant/releases/latest).\n\nFull IsoQuant documentation is available at [ablab.github.io/IsoQuant](https://ablab.github.io/IsoQuant/).\n\n## Supported sequencing data\n\nIsoQuant supports all kinds of long RNA data:\n* PacBio CCS\n* ONT dRNA / ONT cDNA\n* Assembled / corrected transcript sequences\n\nReads must be provided in FASTQ/FASTA format (can be gzipped) or unmapped BAM format. \nIf you have already aligned your reads to the reference genome, simply provide sorted and indexed BAM files.\nIsoQuant expect reads to contain polyA tails. For more reliable transcript model construction do not trim polyA tails.\n\nIsoQuant can also take aligned Illumina reads to correct long-read spliced alignments. However, short reads are _not_\nused to discover transcript models or compute abundances.\n\n\n## Supported reference data\n\nReference genome is mandatory and should be provided in multi-FASTA format (can be gzipped).\n\nReference gene annotation is not mandatory but is likely to increase precision and recall.\nIt can be provided in GFF/GTF format (can be gzipped).\n\nPre-constructed `minimap2` index can also be provided to reduce mapping time.\n\n\n## Citation\nThe paper describing IsoQuant algorithms and benchmarking is available at [10.1038/s41587-022-01565-y](https://doi.org/10.1038/s41587-022-01565-y).\n\nTo try IsoQuant, you can use the data that was used in the publication [zenodo.org/record/7611877](https://zenodo.org/record/7611877).\n\n\n## Feedback and bug reports\nYour comments, bug reports, and suggestions are very welcome. They will help us to further improve IsoQuant. If you have any troubles running IsoQuant, please send us `isoquant.log` from the `\u003coutput_dir\u003e` directory.\n\nYou can leave your comments and bug reports at our [GitHub repository tracker](https://github.com/ablab/IsoQuant/issues) or send them via email: isoquant.rna@gmail.com.\n\n\n\n## Quick start\n\n*   Full IsoQuant documentation is available at [ablab.github.io/IsoQuant](https://ablab.github.io/IsoQuant/).\n\n*   IsoQuant can installed via pip:\n\n        pip install isoquant\n\n*   Via conda (bioconda channel):\n\n        conda create -c conda-forge -c bioconda -n isoquant python=3.12 isoquant\n\n*   Or from GitHub:\n\n        git clone https://github.com/ablab/IsoQuant.git \n        cd IsoQuant\n        git checkout latest\n        pip install -e .\n\nInstallation typically takes no more than a few minutes.\n\n*   If running simply from [the source archive](https://github.com/ablab/IsoQuant/releases/), \nyou will need Python3 (3.8 or higher), [gffutils](https://pythonhosted.org/gffutils/installation.html), [pysam](https://pysam.readthedocs.io/en/latest/index.html), [biopython](https://biopython.org/), [pyfaidx](https://pypi.org/project/pyfaidx/),\n [ssw-py](https://pypi.org/project/ssw-py/), [editdistance](https://pypi.org/project/editdistance/) and some other common Python libraries to be installed. See `requirements.txt` for details. \nYou will also need to have [minimap2](https://github.com/lh3/minimap2) and [samtools](http://www.htslib.org/download/) to be in your `$PATH` variable.\nAll required Python libraries can be installed via: \n\n        pip install -r requirements.txt\n\n*   Verify your installation by running (typically takes less than 1 minute):\n\n        isoquant --test\n\n*   To run IsoQuant on raw FASTQ/FASTA files, use the following command\n\n        isoquant --reference /PATH/TO/reference_genome.fasta \\\n        --genedb /PATH/TO/gene_annotation.gtf \\\n        --fastq /PATH/TO/sample1.fastq.gz /PATH/TO/sample2.fastq.gz \\\n        --data_type (assembly|pacbio_ccs|nanopore) -o OUTPUT_FOLDER\n\n    For example, using the toy data provided within this repository,\n\n        isoquant --fastq isoquant_lib/test_data/chr9.4M.ont.sim.fq.gz \\\n        --reference isoquant_lib/test_data/chr9.4M.fa.gz \\\n        --genedb isoquant_lib/test_data/chr9.4M.gtf.gz \\\n        --data_type nanopore --complete_genedb -p TEST_DATA --output isoquant_test \n\n\n* To run IsoQuant on aligned reads (make sure your BAM is sorted and indexed) use the following command:\n\n        isoquant --reference /PATH/TO/reference_genome.fasta \\\n        --genedb /PATH/TO/gene_annotation.gtf \\\n        --bam /PATH/TO/sample1.sorted.bam /PATH/TO/sample2.sorted.bam \\\n        --data_type (assembly|pacbio_ccs|nanopore) -o OUTPUT_FOLDER\n\n* If using official annotations containing `gene` and `transcript` features use `--complete_genedb` to save time.\n\n* Using reference annotation is optional since version 3.0, you may preform de novo transcript discovery without providing `--genedb` option':\n\n        isoquant --reference /PATH/TO/reference_genome.fasta \\\n        --fastq /PATH/TO/sample1.fastq.gz /PATH/TO/sample2.fastq.gz \\\n        --data_type (assembly|pacbio|nanopore) -o OUTPUT_FOLDER\n\n* If multiple files are provided, IsoQuant will create a single output annotation and a single set of gene/transcript expression tables.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fablab%2FIsoQuant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fablab%2FIsoQuant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fablab%2FIsoQuant/lists"}