jlanga/md_paper

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jlanga/md_paper

jlanga

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md_paper is a skeleton of a paper to be writen in Markdown and compiled into a pdf or docx with pandoc

smsk

Snakemake skeleton - Build workflows with Snakemake

smsk_trinotate

Snakemake workflow to run transdecoder + trinotate

smsk_selection

Snakemake project to predict orthogroups and find patterns of postive selection with orthofinder and fastcodeml

smsk_khmer_trinity

Transcriptome assembly via digital normalization with khmer and Trinity

smsk_popoolation

Snakemake pipeline for Popoolation and Popoolation2

exfi

Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools

smsk_454

Snakemake pipeline for de novo transcriptome assembly with 454 reads

khmer_trinity_snakemake

A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity

snakehooks

git hooks for snakemake pipelines

smsk_annotate

Pipeline to annotate a transcriptome assembly, coding and noncoding parts.

2023-mer_metagenomics

Tutorial and assignments for the course Marine Genomics at IMBRSEA, Plentzia

Jupyter Notebook

smsk_tuxedo2

snakemake files of the tuxedo v2 pipeline from Pertea et al 2016

oari_paper

Selection sweep scan of _Ovis aries_ populations. Version for paper.

smsk_gatk_germline

Snakemake workflow to perform GATK's best practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence