======  Practical Protocols for Probing Protists  ======

==== Unix, Perun and where to find softwares and databases ====

[[ Using UNIX|Using UNIX ]] 

[[ Using perun|Using Perun ]]

[[ RAM and ROM|RAM and CPU memory - Perun Queues ]]

[[ GPU nodes and how to work with them|GPU nodes and how to work with them ]]

[[ Perun and Environments|Perun and Environments ]]

[[ Perun and Custom Environments|Perun and Custom Environments ]]

[[ GitHub repositories of the lab|GitHub repositories of the lab ]]

[[ Other software locations|Other software locations ]]

[[ Databases locations|Databases locations ]]

[[ BLAST protocol|BLAST+ and v5 database user guide ]]

[[BLAST and PLAST|BLAST and PLAST ]] 

[[Taxonomy recovery|Taxonomy recovery from BLAST/PLAST output]]

==== Bioconda ====

[[ Making Bioconda recipes|Making Bioconda recipes ]]

===Tips and Tricks===

The idea of this section is to share command line tips and tricks that you have found made it a lot easier to do bioinformatics work. This can range from basic UNIX things like setting up your terminal environment, configuring your SSH connections or managing your filesystem to explaining new bioinformatics tools and how to work with large scale computer clusters.

Recordings of the **Tips and Tricks** meetings are available for downloading or viewing online  [[https://perun.biochem.dal.ca/downloads/icgvideo/TAT/|here]]

Or directly on Perun, on ''/scratch3/downloads/icgvideo/TAT''


===The Terminal===

[[Setting up your terminal environment ]] 

[[Command line hotkeys]]


===Command line utilities===

[[ls expanded]]

[[wc expanded]]

[[head and tail expanded]]

[[sort expanded]]

[[uniq expanded]]

[[cut expanded]]

[[cat expanded]]

[[nohup]]

[[grep expanded]]

[[awk for tabulated files]]

===SSH===

[[SSH Keys]]

[[Passwords and Passphrases]]

[[The SSH Config]]

===Common Bioinformatics Operations===

[[Viewing tabular BLAST outfiles]]

[[Viewing alignment files]]

[[Handy custom functions]]

[[Manipulating FASTA FILES]]

[[RNA-Seq Processing]]


====DNA Sequence Data Processing====

[[Cleaning of Illumina Paired end reads|[Short reads] Cleaning of Illumina Paired-end reads ]]

[[Short read assembly|[Short reads] Short read assembly ]]

[[depth and breadth of coverage|[Short reads] depth and breadth of coverage]]

[[MINION Sequencing from START to FINISH|[Long reads] MINION Sequencing from START to FINISH]]

[[ASSEMBLING LONG READ DATA|[Long reads] Assembling Long Read Data]]

[[Nanopore tools for polishing|[Long reads] Nanopore tools for polishing]]

[[Decontamination using a metagenomics approach|Decontamination using a metagenomics approach (Anvi’o)]]

[[Decontamination using read classifier (a.k.a Eukfinder)|Decontamination using read classifier (Eukfinder)]]

[[DECONSEQ for decontaminating reads|Decontaminating reads using DECONSEQ]]

[[Binning tools|[Genome] Binning tools ]]

[[Benchmarking Universal Single-Copy Orthologs (BUSCO)|[Genome] Evaluating genome completeness using Benchmarking Universal Single-Copy Orthologs (BUSCO) ]]

[[CGAL|[Genome] Evaluating genome quality using CGAL ]]

[[Using Mitoprot|[Mito genome] Using Mitoprot]]

[[Visualizing mitochondrial genomes|[Mito genome] Visualizing mitochondrial genomes ]]

[[Changing contig or scaffold names in a genome assembly| Changing contig or scaffold names in a genome assembly ]]

[[Extracting a single fasta entry (or multiple) from a multifasta file| Extracting a single fasta entry (or multiple) from a multifasta file]]

[[Getting protein or CDS sequences from a gff file]]

====RNA sequence data, gene expression====

[[Trinity for assembling transcript reads|de novo transcriptome assembly with Trinity]]

[[de novo transcriptome assembly with rnaspades|de novo transcriptome assembly with rnaSPAdes]]

[[Mapping RNAseq data to your genome|[RNA-seq reads] Mapping RNAseq data to your genome]]

[[Evaluating and comparing transcriptome assemblies with rnaQUAST|[Transcriptome] Evaluating and comparing transcriptome assemblies with rnaQUAST]]

[[TransDecoder for transcriptomes|[Transcriptome] TransDecoder for transcriptomes]]

[[Differential gene expression analysis]]

====Gene Prediction====

[[gene_prediction_just_genemark|[Ab initio] Gene prediction with just GeneMark]]

[[gene_prediction_just_augustus|[Ab initio] Gene prediction with just Augustus]]

[[gene_prediction_find_supported_orfs|[RNAseq-informed] Gene prediction with find_supported_orfs.py]]

[[gene_prediction_with_braker2_pipeline|[Pipeline] Gene prediction with Braker2]]

[[gene_prediction_with_funannotate|[Pipeline] Gene prediction with the Funannotate]]

[[automatically_fixing_gene_models|[Fix] Improving gene models with fix_genes_with_false_introns.py]]

[[gene_prediction_curation_with_igv|[Manual Curation] Gene prediction curation with IGV]]

[[From Nanopore to Gene Prediction]]

====Functional annotation====

[[Functional annotation with the Funannotate pipeline]]

[[Finding genes of interest with PANTHER HMMs]]

[[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|Orthologs searches using panther HMMRs]]

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

====Protein structure prediction====

[[Running AlphaFold at scale]]
====Phylogenetic analyses====

[[Multi-gene phylogeny pipeline|[Phylogeny] Multi-gene phylogeny pipeline]]

[[Distinguishin LGT from contaminants|Distinguishing LGT from contaminants]]

[[Running RevBayes with multiple cores]]

====Phylogenomic analyses====

[[Curation of phylogenomic datasets|Curation of phylogenomic datasets]]

====Misc. analyses====

[[Ploidy analysis using ploidyNGS]]

====Programming languages====

[[python_resources|Python Resources]]

====Bioinformatics Q&A====

[[Unix/shell|[Q&A] Real cases of bash/shell scripts「Ongoing」]]

[[Q&A others]]

====Bioinformatics and Trivia====

[[Bioinformatics_essay|Do Bioinformaticians have naming regrets?]]

[[Bioinformatics_essay0|A little of what you fancy does you good!]]


[[Playground]]

====Dokuwiki maintenance====

[[Who looks after which page]]

====== Project Documentation ======

[[ Blastocystis orf160 ]]
This could possibly be an interesting project for a future undergraduate student