Scripts and supplemental material for the assembly and analysis of Sapria genome.
Disclaimer: Although we welcome re-use of these materials, except where noted the code we are sharing here is specific to this project and to the Harvard compute cluster. Filenames and paths are often hard-coded in scripts, and software versions/dependencies are often managed via calls to the Harvard Cannon cluster Lmod system.
The content of each subdirectory is listed as follows. For detailed description and scripts, please see the README file within each directory.
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sapria_genome_assembly
kmer-based genome size estimation
de novo assembly with Supernova using 10X library
scaffolding with the ARKS-LINKS pipeline using long-read data
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validation_of_genome_assembly
mapping Illumina, nanopore, and transcripts to the assembly
assembly of unmapped Illumina reads
BUSCO assessment
missing BUSCO simulation in the Manihot genome
non-repetitive region size estimation based on read coverage
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annotation
de novo repeat annotation with repeatModeler and repeatMasker
gene prediction with MAKER
pseudogene annotation with the Shiu Lab pipeline
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ortholog_clustering
ortholog group assignment with OrthoFinder
pseudogenes ortholog group assignment for phylogenetic inference
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intron_turnover
intron length and position characterization
intron turnover rate based on cross-species protein alignment
correlation test of maximum intron length and dN/dS ratio
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selection
dN/dS ratio calculation using PAML
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tetrastigma_genome_assembly
nanopore de novo assembly with minimap-miniasm
nanopore de novo assembly with CANU
assembly merging using Quickmerge
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HGT_pairwiseDivergence (Contributor: Dr. Brian Arnold)
Genome alignment of 10 plant species using Cactus
Sliding window-based analysis of pairwise divergence to detect HGT
Grouping nearby HGT genomic windows into longer blocks
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phylogenetic_assessment_of_HGT
alignment and gene tree reconstruction
custom python script to identify HGT based on phylogeny