Description

Low coverage support

Methods

This file contains regions with low coverage support in HiFi, CLR, and ONT platforms.

Reads were aligned with Winnowmap 1.11, with the read alignments downloadable here.

Primary read alignments have been processed with asset commit ver. 0133f268eebf308a1c3eb356b564550526465157, and regions meeting the following criteria are reported in each platform:

  • Less than 10 reads aligned
  • Merged when regions are less than 1kbp apart
  • Exclude low coverage at both 1kbp ends of each chromosome due to natural coverage drop
  • Exclude low coverage overlapping rDNA gaps + 10bp around

    Two additional files are provided using the same criteria above, except the ONT reads were prefiltered from the primary alignments.

  • low_coverage.30k.bed : Using ONT reads greater than 30 kbp
  • low_coverage.100k.bed : Using ONT reads greater than 100 kbp

    Display Conventions and Configuration

  • HIFI only : 204,0,0 (red)
  • CLR only : 255,153,0 (dark yellow)
  • ONT only : 0,102,255 (dark blue)
  • HIFI & ONT : 102,0,204 (dark purple)
  • CLR & HIFI : 153,0,51 (dark red)
  • CLR & ONT : 204,0,204 (dark pink)
  • CLR & HiFi & ONT : 0,0,0 (black)

    Data access

    https://github.com/marbl/CHM13-issues

    Release history

    1. 2021 Feb 23. Internal release

    Contacts

    Credits