Review freeze

GraffiTE version at the time of the second round of peer reviews.

GraffiTE - publication freeze

GraffiTE version used in preparing "GraffiTE: a unified framework to analyze transposable element insertion polymorphisms using genome-graphs".

v0.2 (beta)

• beta 0.2 (11-11-22):
  • adds two new read aligners: giraffe (short read optimized, works also with long-reads) and graphAligner (long-read, error-prone compliant).
    • usage: --graph_method [pangenie/giraffe/graphaligner] default: pangenie (short accurate reads)
  • adds --vcf input option: requires a sequence resolved (REF and ALT allele sequences in VCF). Will bypass genome alignments and proceed with repeat annotations, TSD search, and reads mapping (optional).
  • adds --graffite_vcf input option: requires a VCF created by GraffiTE (in the outputs 3_TSD_search/pangemome.vcf). Will skip all steps but read mapping.
  • bug fix: remove the dependency to biomartr
  • add readthedocs

v0.1 (beta)

update README