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https://github.com/morispi/LRez

Standalone tool and library allowing to work with barcoded linked-reads
https://github.com/morispi/LRez

10x 10x-genomics 10xgenomics barcode barcodes bioinformatics haplotagging index linked linked-reads reads stlfr tell-seq

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Standalone tool and library allowing to work with barcoded linked-reads

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# LRez



LRez 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.



Presently, 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):

  - 10x Genomics

  - Haplotagging

  - stLFR

  - TELL-Seq



LRez has different functionalities such as comparing regions pairs or contigs extremities to retrieve their common barcodes and extracting barcodes from given regions

of 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.

In can thus be used in different applications, such as variant calling or scaffolding.



Requirements

--------------



  - A Unix based operating system.

  - g++, minimum version 5.5.0.

  - CMake, minimum version 2.8.2.

  - zlib, minimum version 1.2.11.

  

Installation from source

--------------



Clone the LRez repository, along with its submodules with:



  ```bash

  git clone --recursive https://github.com/morispi/LRez

  ```



Then run the install.sh script:



  ```bash

  ./install.sh

  ```



The 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.



Installation from conda

--------------



Alternatively, LRez is also distributed as a bioconda package, which can be installed with:



```bash

conda install -c bioconda lrez

```

  

Using the toolkit

--------------



### Usage



`LRez [SUBCOMMAND]`



where [SUBCOMMAND] can be one of the following:



  - compare:     Compute the number of common barcodes between pairs of regions, or between pairs of contigs' extremities

  - extract:     Extract the barcodes from a given region of a BAM file

  - stats:       Retrieve general stats from a BAM file

  - index bam:   Index the offsets or occurrences positions of the barcodes contained in a BAM file

  - query bam:   Query the barcodes index to retrieve alignments in a BAM file, given a barcode or list of barcodes

  - index fastq: Index the offsets of the barcodes contained in a fastq file

  - query fastq: Query the barcodes index to retrieve alignments in a fastq file, given a barcode or list of barcodes



### Subcommands



A description of each subcommand as well as its options is given below.



#### Compare



`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.



      --bam STRING, -b STRING:      BAM file containing the alignments

      --index STRING, -i SRING:     Barcodes offsets index built with the index bam subcommand

      --region STRING, -r STRING:   File containing regions of interest in format chromosome:startPosition-endPosition

      --contig STRING, -c STRING:   Contig of interest

      --contigs STRING, -c STRING:  File containing a list of contigs of interest

      --size INT, -s INT:           Size of contigs' extremities to consider (optional, default: 1000) 

      --output STRING, -o STRING:   File where to output the results (optional, default: stdout)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Extract



`LRez extract` allows to extract the list of barcodes in a given region of a BAM file.



      --bam STRING, -b STRING:      BAM file to extract barcodes from

      --region STRING, -r STRING:   Region of interest in format chromosome:startPosition-endPosition

      --all, -a:                    Extract all barcodes

      --output STRING, -o STRING:   File where to output the extracted barcodes (optional, default: stdout)

      --duplicates, -d:             Include duplicate barcodes (optional, default: false)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Stats



`LRez stats` allows to retrieve general stats from the BAM file.



      --bam STRING, -b STRING:      BAM file to extract barcodes from

      --regions INT, -r INT:        Number of regions to consider to define stats (optional, default: 1000)

      --size INT, -s INT:           Size of the regions to consider (optional, default: 1000)

      --output STRING, -o STRING:   File where to output the extracted barcodes (optional, default: stdout)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Index BAM



`LRez index bam` allows to index the offsets or occurrences positions of the barcodes contained in a BAM file.



      --bam STRING, -b STRING:      BAM file to index

      --output STRING, -o STRING:   File where to store the index

      --offsets, -f:                Index the offsets of the barcodes in the BAM file

      --positions, -p:              Index the (chromosome, begPosition) occurrences positions of the barcodes

      --primary, -r:                Only index barcodes that appear in a primary alignment (optional, default: false)

      --quality INT, -q INT:        Only index barcodes that appear in an alignment of quality higher than this number (optional, default: 0)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Query BAM



`LRez query bam` allows to query a barcodes index and a BAM file to retrieve alignments containing the query barcodes.



      --bam STRING, -b STRING:      BAM file to search

      --index STRING, -i STRING:    Barcodes offsets index, built with the index bam subcommand, using the -f option.

      ---query STRING, -q STRING:   Query barcode to search in the BAM / index

      --list STRING, -l STRING:     File containing a list of barcodes to search in the BAM / index

      --output STRING, -o STRING:   File where to output the extracted alignments (optional, default: stdout)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Index fastq



`LRez index fastq` allows to index the offsets of the barcodes contained in a fastq file.



      --fastq STRING, -f STRING:    Fastq file to index

      --output STRING, -o STRING:   File where to store the index

      --gzip, -g:                   Fastq file is gzipped (optional, default: false)

      --threads INT, -t INT:        Number of threads to use (optional, default: 1)



#### Query fastq



`LRez query fastq` allows to query a barcodes index and a fastq file to retrieve alignments containing the query barcodes.



      --fastq STRING, -f STRING:                Fastq file to search

      --index STRING, -i STRING:                Barcodes index, built with the index fastq subcommand

      --query STRING, -q STRING:                Query barcode to search in the fastq file and the index

      --list STRING, -l STRING:                 File containing a list of barcodes to search in the fastq file and the index

      --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

      --output STRING, -o STRING:               File where to output the extracted reads (optional, default: stdout)

      --gzip, -g:                               Fastq file is gzipped (optional, default: false)

      --threads INT, -t INT:                    Number of threads to use (optional, default: 1)



Using the API

--------------



Complete 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.



Notes

--------------



LRez has been developed and tested on x86-64 GNU/Linux.          

Support for any other platform has not been tested.



Authors

--------------



Pierre Morisse, Claire Lemaitre and Fabrice Legeai.



Reference

--------------



Pierre 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



Contact

--------------



You can report problems and bugs as issues on this repository : https://github.com/morispi/LRez/issues