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Júlia Wiggeshoff (juliawiggeshoff)

juliawiggeshoff

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Júlia Wiggeshoff's repositories

AugusMake

The AugusMake pipeline is a Snakemake-based workflow for generating gene annotations using the Augustus software. AugusMake can perform gene predictions using any combination of the three methods: ab initio, with extrinsic hints, or by training a new species.

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singularity-recipes

Recipes for Singularity

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astral-species-tree

This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 bootstrap replicates for each tree. Then, consensus trees are produced and combined to infer a species tree following the multispecies coalescent model with ASTRAL. Imported from my GitLab.

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rna-seq-2x-de-novo-assembly

Snakemake workflow to de novo assemble transcriptomes with two software, Trinity and Shannon. Imported from my GitLab.

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supermatrix-tree

Snakemake workflow that concatenate MSA files into a supermatrix and calculates a maximum likelihood tree. Imported from my GitLab

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VCFpytools

Assortment of VCF processing scripts

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