MINTIE Versions Save

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

v0.4.2

1 year ago

Reference update

v0.4.1

1 year ago

Release to trigger bioconda rebuild (0.4.0 failed due to CircleCI issue).

v0.4.0

2 years ago

Support for single-end data.

v0.3.9

2 years ago

Added wrapper script.

v0.3.8

2 years ago

Fix for setting up references

v0.3.7

2 years ago

Portability fixes

v0.3.6

2 years ago
  • Removed legacy viz functions
  • filter_fasta.py optimisation

v0.3.5

2 years ago
  • Added 40bp sequence output for each variant's position (20bp flanking either side of each position)
  • INDEL simulation now allows setting constant size
  • Improved retained intron detection
  • Minor fixes and improvements

v0.3.0

3 years ago
  • Numerous bug fixes
  • Compatibility for salmon v1+
  • Added intragenic rearrangement (IGR) variant type
  • Motif checking leniency (+ motifs are now returned in an output column)
  • Variant sizes have been fixed for numerous splice variants and TSVs
  • Check kmer params when running assembly
  • Tweaks to default config parameters

v0.2.0

3 years ago
  • set --max-intronlength-ends to 500kb, this is due to cases where GMAP soft-clips the terminal exon(s) if they are over 10kb (default value)
  • set chimeric alignment option to match min clip length
  • consider partial novel junctions when checking for presence of novel intron (may also be novel exon). This may occur in cases of overlapping exons that can obscure novel exons.