=====This page is quite obsolete - Jason=====

Distinguishin LGT from contaminants

Using UNIX -Bruce

BLAST and PLAST -Dayana

Taxonomy recovery

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

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 -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

Using Mitoprot

Perun and Environments -Bruce

Other software locations -Bruce

Databases locations -Dayana

Gene prediction framework -Dayana

CGAL

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

From Nanopore to Gene Prediction 

Short read assembly 

Python Resources

depth and breadth of coverage

Binning tools 

Visualizing mitochondrial genomes