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Releases: Ensembl/plant-scripts

04102024

25 Oct 07:44
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This release ships with get_pangenes.pl version 04102024.

Main changes are:
25092024: added section 'Example 6: estimation of haplotype diversity'
03102024: get_pangenes.pl expects min 95% sequence identity for WGA-based gene alignments, as in GET_HOMOLOGUES-EST, to help avoid diverged tandem copies
04102024: get_pangenes.pl now set MAXDISTNEIGHBORS=2, neighbor genes in a cluster cannot be more than 2 genes away

11012024

08 Feb 16:22
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This release ships with updates to GET_PANGENES: code changes since the publication of the manuscript, involving:

15112023

16 Nov 07:31
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This release ships with updates to:

  • GET_PANGENES: code and documentation changes since the publication of the manuscript, involving improved handling of input GFF files and calculation of overlap coordinates from WGA segments in different strands.

  • REST-based recipes.

pangenes_benchmark

03 Apr 14:40
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Pangene sets of Arabidopsis (ACK), rice, wheat and barley datasets produced while benchmarking get_pangenes as described at https://doi.org/10.1186/s13059-023-03071-z and https://www.biorxiv.org/content/10.1101/2023.01.03.520531v2

The HOWTO* files contain the actual commands required to produce these results with the input FASTA & GFF files (32GB), which should be first be downloaded from DOI

The source code was archived as DOI but has been updated since.

test_rice

04 Jan 20:12
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Toy dataset to test the scripts for pan-gene analysis.

nrTEplants

16 Feb 12:23
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Release 0.3 (Jun2020) the nrTEplants library of plant transposable elements which minimizes overlap with sequence containing protein domains known to be part of NLR genes. This sequence set was computed after combining TREP, SINEbase, REdat, RepetDB, EDTArice, EDTAmaize, SoyBaseTE, TAIR10TE, SunflowerTE, MelonTE, RosaTE and SUNREP and obtaining a non-redundant collection with GET_HOMOLOGUES-EST.

Check the code and documentation at https://github.com/Ensembl/plant_tools/tree/master/bench/repeat_libs

Citation: Contreras-Moreira,B., Filippi,C.V., Naamati,G., Girón,C.G., Allen,J.E. and Flicek,P. (2021) Efficient masking of plant genomes by combining kmer counting and curated repeats Genomics. Plant Genome https://doi.org/10.1002/tpg2.20143

23102020

23 Oct 13:11
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This release was created to obtain a DOI from Zenodo