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Distinguishin LGT from contaminants

Using UNIX -Bruce

BLAST and PLAST -Dayana

Taxonomy recovery -Dandan

Using perun -Bruce

Decontamination using a metagenomics approach -Dayana

Decontamination using read classifier (a.k.a Eukfinder) -Dayana

Multi-gene phylogeny pipeline - Shelby

TransDecoder for transcriptomes

Cleaning of Illumina Paired end reads -Dandan

Benchmarking Universal Single-Copy Orthologs (BUSCO) -Dandan

Trinity for assembling transcript reads

Differential gene expression analysis

Nanopore tools for polishing

Search Protocol for Orthologs of Components of Key molecular systems (SPOCK)...\\ SORRY this is not up and running yet. Please complain with Dayana!

Ortologs searches using panther HMMRs -Dayana

DECONSEQ for decontaminating reads

MINION Sequencing from START to FINISH

ASSEMBLING LONG READ DATA

Dayana Salas - Utility scripts(taxonomy, coloring trees, phylogenetics, mixture models, domain architecture and more) -Dayana

Mapping RNAseq data to your genome

Changing contig or scaffold names in a genome assembly -Dandan

Using Mitoprot

Perun and Environments -Bruce

Other software locations -Bruce

Databases locations -Dayana

Gene prediction framework -Dayana

CGAL -Dandan

Extracting a single fasta entry (or multiple) from a multifasta file -Bruce

From Nanopore to Gene Prediction

Short read assembly -Dandan

Python Resources

depth and breadth of coverage -Dandan

Binning tools -Dandan

Visualizing mitochondrial genomes -Dandan

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