Add platform support

[pontushojer]

Add support to other available linked-read plattforms:

• [x] CPTv2 (Will not be added as no longer relevant)
• [x] stLFR=BGI linked reads
• [x] Tell-seq
• [ ] Haplotagging

[pontushojer]

stLFR

I am currently working on integrating stLFR reads.

Article: https://genome.cshlp.org/content/29/5/798.full

Test dataset: ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/stLFR/

This is from a GIAB where they have included a stLFR dataset on NA24385 (10x Genomics control), the same we have been using for our data. The files are already demultiplexed using the the tool stLFR_read_demux that were developed for their paper.

[pontushojer]

CPTv2

Articles:

• CPTv2-seq, Zhang et a. 2017
• CPT-seq, Amini et al. 2014

Test dataset:

• CPT-seq: Project data for NA12878
  • Download using SRA-Toolkit: ./fastq-dump SRR1554094 -G -O NA12878 --> one file per barcode.
• CPTv2-seq: No data available, link in paper not working.

[pontushojer]

TELL-seq

Article: Chen et al. 2019

Test dataset: https://www.ncbi.nlm.nih.gov/sra/SRX7264481[accn]

Dataset is NA24385.

[pontushojer]

Haplotagging

New technology has recently been introduced.

Article: Meier et al. 2020

Test dataset: None yet, dataset will probably be NA12878.