Code for de novo assembly of unmapped reads and calling of ancestral sequences, as shown in Taliun et al., 2019

Requirements

• In $PATH:

  • makecalls_bin/
  • assembly_bin/
  • Python 2.7+
  • Perl 5
  • BWA v0.7.12+
  • SAMtools v1.7+
  • BEDTools v2.25.0+
  • Cutadapt v1.16+
  • liftOver
  • GEM pre-release 3
  • AGE (age_align binary, more specifically)
  • ABySS v2.0.2

• UCSC references indexed for BWA-MEM:

  • hg38
  • gorGor5
  • panPan2
  • panTro6
  • ponAbe3

• Reference indexed for GEM-mapper:

  • hg38 with only chromosomes 1-22,X,Y and hard-masked PAR on chromosome Y.

• UCSC chain files:

  • gorGor5ToHg38.over.chain
  • panPan2ToHg38.over.chain
  • panTro6ToHg38.over.chain
  • ponAbe3ToHg38.over.chain

• phiX index for GEM-mapper (provided in assembly_res/)