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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)…
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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