From e141f9e601a5f33f16246e9dfcd336b19b482b2e Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 17:53:17 -0400 Subject: [PATCH] Updated Utilities (markdown) --- Utilities.md | 62 ++++++++++++++++++++++++++-------------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/Utilities.md b/Utilities.md index 11fe868..66479f3 100644 --- a/Utilities.md +++ b/Utilities.md @@ -1,33 +1,33 @@ -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 | \ No newline at end of file +| 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 | \ No newline at end of file