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Distinguishin LGT from contaminants

Using UNIX -Bruce

BLAST and PLAST

Taxonomy recovery

Using perun -Bruce

Decontamination using a metagenomics approach

Multi-gene phylogeny pipeline

TransDecoder for transcriptomes

Cleaning of Illumina Paired end reads

Benchmarking Universal Single-Copy Orthologs (BUSCO)

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

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)

Mapping RNAseq data to your genome

Changing contig or scaffold names in a genome assembly

Using Mitoprot

Perun and Environments -Bruce

Other software locations -Bruce

Databases locations

Gene prediction framework

CGAL

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

From Nanopore to Gene Prediction

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