tunazislam / rextal

REXTAL: Regional Extension of Assemblies Using Linked-Reads

REXTAL

To run REXTAL for 18p:

The key input data is 10X Genomics linked-reads from individual human genomes, in our case from the genome of a publically available cell line GM19440. Our dataset has approximately 1.49 billion 10X Genomics linked-reads in paired-end format, with each read about 150 bp.

1. Preprocessing of REXTAL:

2. We processed the raw 10X Genomics data using Long Ranger Basic software developed by 10X Genomics (and freely available to any researcher) to generate barcode-filtered 10XG linked-reads. The Long Ranger basic pipe-line performs basic read and barcode processing including read trimming, barcode error correction, barcode whitelisting, and attaching barcodes to reads. Please see the file Longranger_run.sh, Longranger_postprocessing.sh.

   i) To run Longranger Basic:

   sbatch Longranger_run.sh
   

   ii) Longranger Basic generates output in .fastq file. We did postprocessing of that .fastq file.

   sbatch Longranger_postprocessing.sh
   

3. extract 18p 1-copy, bait, segmental duplication from UC genome browser

4. Use online RepeatMasker (RM)

5. Use tandem repeat finder

6. python code for wrapping the line (if needed) (text_wrap_affter_tandem_repeat_finder.py)

7. Run REXTAL pipeline

   1. We have input fasta file (barcode-filtered 10XG linked-reads file, size: almost 600 GB) in a folder named /scratch-lustre/tisla003/Original_Data/longranger/longranger_output/barcoded_output/outs/nospace_modified_barcode_fasta_big.fasta. I used the directoy where I kept, you can rename it according to yours.
   2. We have another input fasta file (Hg38 extracted from UC genome browser ) in a folder named /scratch-lustre/tisla003/Original_Data/summer2018/input/18p_Bait_RM_tandem.fasta. I used the directoy where I kept, you can rename it according to yours.
   3. Keep the files pipeline_18p.sh (main REXTAL pipeline file), extract_bc_range.py, cluster_bc_multiple_3_70.py, file_match_3_70_L001.sh, file_match_3_70_L002.sh, get_line_number_L001.py, get_line_number_L002.py, extract_I1_L001_3_70.py, extract_R1_L001_3_70.py, extract_R2_L001_3_70.py, extract_I1_L002_3_70.py, extract_R1_L002_3_70.py, extract_R2_L002_3_70.py in a directory i.e. 18p.
   4. In SSH type:

   dos2unix pipeline_18p.sh
   chmod +x pipeline_18p.sh
   

   5. Run the job script:

   sbatch pipeline_18p.sh
   

8. Output: You will find output of REXTAL in ../18p/supernova_assembly_18/ here named as 18p_pseudohap2.1.fasta and 18p_pseudohap2.2.fasta.

Dependency:

1. To run REXTAL you have to install Longranger Basic, BLAT, 10X Genomics Supernova (assembler) in your server.

2. To run other subtelomeric region for example 16p, 16q, 17p, 17q, 20q, 22q etc. you have to rename contents of file with corresponding subtelomere name. These files: pipeline_(corresponding_subtelomere)p.sh (main REXTAL pipeline file), extract_bc_range.py, cluster_bc_multiple_3_70.py, file_match_3_70_L001.sh, file_match_3_70_L002.sh, get_line_number_L001.py, get_line_number_L002.py, extract_I1_L001_3_70.py, extract_R1_L001_3_70.py, extract_R2_L001_3_70.py, extract_I1_L002_3_70.py, extract_R1_L002_3_70.py, extract_R2_L002_3_70.py.

Here is the Publication link of our paper:

REXTAL: https://link.springer.com/chapter/10.1007/978-3-319-94968-0_6

Analysis of REXTAL: https://ieeexplore.ieee.org/document/8703093

You can read the pdf from my website:

REXTAL: https://tunazislam.github.io/files/REXTAL_ISBRA2018.pdf

Analysis of REXTAL: https://tunazislam.github.io/files/REXTAL_QUAST_TCBB2019.pdf

Presentation Slide: https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnx0dW5hemlzbGFtfGd4OjY5YjVjMjc1MjBjN2FiNQ