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Updated Utilities (markdown)

Katzlab 2024-08-09 17:53:17 -04:00
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Utilities.md

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PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: basic statistics, composition tools, MSA tools, gene tree description, and contamination removal.
PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: basic statistics, composition tools, MSA tools, gene tree description, and contamination removal
A summary of some of the scripts is divided by category here
| [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output |
| ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- |
| Assess_transcriptomes_v2.0.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. |
| Cluster_v2.0.py | Clusters sequences in a fasta file | Clustered fasta files |
| GetTaxonomy_v1.0.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy |
| GetUniqueTaxa_v1.0.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa |
| Plot_transcriptomes_v2.0.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. |
| QuerySRA_v1.0.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. |
| ReadMapping_v2.0.py | Maps a group of trimmed reads to a reference | Sam/Bam files. |
| SeqLenToCsv_v1.0.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. |
| SharedOGs_v1.0.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families |
| | | |
| | | |
| CUB_v2.1.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition |
| GC_identifier_v1.0.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID |
| PlotComps_v2.0.r | Produces GC3 width plots | GC3 width plots |
| Plotcomps_SppName_v1.0.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots |
| | | |
| | | |
| BacktranslateAlignment.py | Produces new nucleotide alignment from an amino acid alignment | Aligned nucelotide file |
| CountTaxonOccurence_v2.0.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa |
| friendlessness_v2.0.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics |
| Gappiness_v2.0.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics |
| GuidanceWrapper_v2.1.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files |
| | | |
| | | |
| CladeSizes_v2.0.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes |
| ColorByClade_v2.1.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees |
| ContaminationBySisters_v2.2.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship |
| RenameTips_v1.0.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees |
| Input | [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output |
| ----------------------------- | ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- |
| Assembly and fasta tools | Assess_transcriptomes_v2.0.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. |
| | Cluster_v2.0.py | Clusters sequences in a fasta file | Clustered fasta files |
| | GetTaxonomy_v1.0.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy |
| | GetUniqueTaxa_v1.0.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa |
| | Plot_transcriptomes_v2.0.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. |
| | QuerySRA_v1.0.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. |
| | ReadMapping_v2.0.py | Maps a group of trimmed reads to a reference | Sam/Bam files. |
| | SeqLenToCsv_v1.0.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. |
| | SharedOGs_v1.0.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families |
| | | | |
| Sequence composition analysis | CUB_v2.1.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition |
| | GC_identifier_v1.0.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID |
| | PlotComps_v2.0.r | Produces GC3 width plots | GC3 width plots |
| | Plotcomps_SppName_v1.0.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots |
| | | | |
| MSA tools | BacktranslateAlignment.py | Produces new nucleotide alignment from an amino acid alignment | Aligned nucelotide file |
| | CountTaxonOccurence_v2.0.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa |
| | friendlessness_v2.0.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics |
| | Gappiness_v2.0.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics |
| | GuidanceWrapper_v2.1.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files |
| | | | |
| Gene tree description | CladeSizes_v2.0.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes |
| | ColorByClade_v2.1.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees |
| | ContaminationBySisters_v2.2.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship |
| | RenameTips_v1.0.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees |
| | | | |
| Stand-alone clade grabbing | CladeGrabbing_v2.1.py | Selects clades of interest from trees using taxonomic specifications | Phylogenetic trees |