{"id":13408225,"url":"https://github.com/morispi/LRez","last_synced_at":"2025-03-14T12:32:25.088Z","repository":{"id":52100968,"uuid":"341265783","full_name":"morispi/LRez","owner":"morispi","description":"Standalone tool and library allowing to work with barcoded 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LRez\n\nLRez provides a standalone tool allowing to work with barcoded linked-reads such as 10X Genomics data, as well as library allowing to easily use it in other projects.\n\nPresently, it is directly compatible with the following linked-reads technologies, given the barcodes are reported using the `BX:Z` tag (if this is not the case, pre-processing scripts are given in the [utils/](utils/) directory):\n  - 10x Genomics\n  - Haplotagging\n  - stLFR\n  - TELL-Seq\n\nLRez has different functionalities such as comparing regions pairs or contigs extremities to retrieve their common barcodes and extracting barcodes from given regions\nof a BAM file, as well as indexing and querying both BAM and FASTQ files to quickly retrieve reads or alignments sharing a given barcode or list of barcodes.\nIn can thus be used in different applications, such as variant calling or scaffolding.\n\nRequirements\n--------------\n\n  - A Unix based operating system.\n  - g++, minimum version 5.5.0.\n  - CMake, minimum version 2.8.2.\n  - zlib, minimum version 1.2.11.\n  \nInstallation from source\n--------------\n\nClone the LRez repository, along with its submodules with:\n\n  ```bash\n  git clone --recursive https://github.com/morispi/LRez\n  ```\n\nThen run the install.sh script:\n\n  ```bash\n  ./install.sh\n  ```\n\nThe installation script will build dependencies, the binary standalone in the `bin` folder, as well as the library, allowing to use LRez in other projects, in the `lib` folder.\n\nInstallation from conda\n--------------\n\nAlternatively, LRez is also distributed as a bioconda package, which can be installed with:\n\n```bash\nconda install -c bioconda lrez\n```\n  \nUsing the toolkit\n--------------\n\n### Usage\n\n`LRez [SUBCOMMAND]`\n\nwhere [SUBCOMMAND] can be one of the following:\n\n  - compare:     Compute the number of common barcodes between pairs of regions, or between pairs of contigs' extremities\n  - extract:     Extract the barcodes from a given region of a BAM file\n  - stats:       Retrieve general stats from a BAM file\n  - index bam:   Index the offsets or occurrences positions of the barcodes contained in a BAM file\n  - query bam:   Query the barcodes index to retrieve alignments in a BAM file, given a barcode or list of barcodes\n  - index fastq: Index the offsets of the barcodes contained in a fastq file\n  - query fastq: Query the barcodes index to retrieve alignments in a fastq file, given a barcode or list of barcodes\n\n### Subcommands\n\nA description of each subcommand as well as its options is given below.\n\n#### Compare\n\n`LRez compare` allows to compute the number of common barcodes between all possibles pairs of a given list of regions, or between a given contig's extremities and all other contigs' extremities.\n\n      --bam STRING, -b STRING:      BAM file containing the alignments\n      --index STRING, -i SRING:     Barcodes offsets index built with the index bam subcommand\n      --region STRING, -r STRING:   File containing regions of interest in format chromosome:startPosition-endPosition\n      --contig STRING, -c STRING:   Contig of interest\n      --contigs STRING, -c STRING:  File containing a list of contigs of interest\n      --size INT, -s INT:           Size of contigs' extremities to consider (optional, default: 1000) \n      --output STRING, -o STRING:   File where to output the results (optional, default: stdout)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Extract\n\n`LRez extract` allows to extract the list of barcodes in a given region of a BAM file.\n\n      --bam STRING, -b STRING:      BAM file to extract barcodes from\n      --region STRING, -r STRING:   Region of interest in format chromosome:startPosition-endPosition\n      --all, -a:                    Extract all barcodes\n      --output STRING, -o STRING:   File where to output the extracted barcodes (optional, default: stdout)\n      --duplicates, -d:             Include duplicate barcodes (optional, default: false)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Stats\n\n`LRez stats` allows to retrieve general stats from the BAM file.\n\n      --bam STRING, -b STRING:      BAM file to extract barcodes from\n      --regions INT, -r INT:        Number of regions to consider to define stats (optional, default: 1000)\n      --size INT, -s INT:           Size of the regions to consider (optional, default: 1000)\n      --output STRING, -o STRING:   File where to output the extracted barcodes (optional, default: stdout)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Index BAM\n\n`LRez index bam` allows to index the offsets or occurrences positions of the barcodes contained in a BAM file.\n\n      --bam STRING, -b STRING:      BAM file to index\n      --output STRING, -o STRING:   File where to store the index\n      --offsets, -f:                Index the offsets of the barcodes in the BAM file\n      --positions, -p:              Index the (chromosome, begPosition) occurrences positions of the barcodes\n      --primary, -r:                Only index barcodes that appear in a primary alignment (optional, default: false)\n      --quality INT, -q INT:        Only index barcodes that appear in an alignment of quality higher than this number (optional, default: 0)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Query BAM\n\n`LRez query bam` allows to query a barcodes index and a BAM file to retrieve alignments containing the query barcodes.\n\n      --bam STRING, -b STRING:      BAM file to search\n      --index STRING, -i STRING:    Barcodes offsets index, built with the index bam subcommand, using the -f option.\n      ---query STRING, -q STRING:   Query barcode to search in the BAM / index\n      --list STRING, -l STRING:     File containing a list of barcodes to search in the BAM / index\n      --output STRING, -o STRING:   File where to output the extracted alignments (optional, default: stdout)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Index fastq\n\n`LRez index fastq` allows to index the offsets of the barcodes contained in a fastq file.\n\n      --fastq STRING, -f STRING:    Fastq file to index\n      --output STRING, -o STRING:   File where to store the index\n      --gzip, -g:                   Fastq file is gzipped (optional, default: false)\n      --threads INT, -t INT:        Number of threads to use (optional, default: 1)\n\n#### Query fastq\n\n`LRez query fastq` allows to query a barcodes index and a fastq file to retrieve alignments containing the query barcodes.\n\n      --fastq STRING, -f STRING:                Fastq file to search\n      --index STRING, -i STRING:                Barcodes index, built with the index fastq subcommand\n      --query STRING, -q STRING:                Query barcode to search in the fastq file and the index\n      --list STRING, -l STRING:                 File containing a list of barcodes to search in the fastq file and the index\n      --collectionOfLists STRING, -c STRING:    File of files (FOF) e.g. file containing files' names of lists of barcodes to search in the fastq file and the index\n      --output STRING, -o STRING:               File where to output the extracted reads (optional, default: stdout)\n      --gzip, -g:                               Fastq file is gzipped (optional, default: false)\n      --threads INT, -t INT:                    Number of threads to use (optional, default: 1)\n\n\nUsing the API\n--------------\n\nComplete documentation of the different API functions is provided at https://morispi.github.io/LRez/files.html. Additionnal information and usage examples are provided on the Wiki page https://github.com/morispi/LRez/wiki.\n\nNotes\n--------------\n\nLRez has been developed and tested on x86-64 GNU/Linux.          \nSupport for any other platform has not been tested.\n\nAuthors\n--------------\n\nPierre Morisse, Claire Lemaitre and Fabrice Legeai.\n\nReference\n--------------\n\nPierre Morisse, Claire Lemaitre, Fabrice Legeai. LRez: C++ API and toolkit for analyzing and managing Linked-Reads data.  Bioinformatics Advances, vbab022, https://doi.org/10.1093/bioadv/vbab022\n\n\nContact\n--------------\n\nYou can report problems and bugs as issues on this repository : https://github.com/morispi/LRez/issues\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmorispi%2FLRez","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmorispi%2FLRez","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmorispi%2FLRez/lists"}