Functional Annotation of ANimal Genomes (FAANG) Project

— A coordinated international action to accelerate Genome to Phenome

Terms of reference

1. Purpose
   • To agree and define standard pipelines for the analysis of FAANG data, with the aim that data sets are comparable because they have been analysed using the same pipeline.
   • These pipelines to include software names, versions and parameter sets and the order in which they should be applied. Software chosen should be "industry standard"
   • The group should work together to investigate methods to integrate the primary analysis results to high level summaries of functional state
   • To communicate with the "Metadata and Data Sharing" group to ensure samples come with all sample and experimental metadata needed to run said pipelines.
   • To communicate with the "Samples, Assays and Animals group to ensure we know the number and type of samples that will arrive.
   • To communicate with the "Samples, Assays and Animals" group to define metrics which we will feed back regarding the quality of the data we receive and the quality of the analysis that has been carried out.
   • To define computational data standards and make recommendations to the Samples, Assays and Animals" group about minimal experimental standards in terms of depth, read length, pairedness etc
   • The group will be responsible for defining standard datasets such as reference genome, gene sets, mappability sets/black lists
2. Membership
   • Executive: Mick Watson, James Reecey
   • Members of the faang-analysis mailing list
3. Meetings
   • The group will meet as required via Zoom and will engage in discussion over email via the faang-analysis mailing list.
   • Regular monthly meetings will be scheduled
4. Accountability
   • The group is accountable to the international FAANG steering committee
5. Method
   • Leads for each data type/analysis task (e.g. RNA-Seq, ChIP-Seq etc) will be identified and the lead will work with others in the group to create a proposal for a standard pipeline for that data type. The lead will report back to the group for approval of the proposal
   • The wider group will then be asked to agree to the adoption of that pipeline.
   • The pipeline should include software names and versions and all parameter sets. The software chosen should be "industry standard". The pipeline should include any filtering, pre- and post- processing steps
   • Periodic reviews of each pipeline will be carried out via this group. Any member can propose a change.
   • Before re-analysis of large scale datasets is started (e.g when triggered by genome assembly updates) methodology will be reviewed and updated based on newer methods or better understanding of the data
6. Review
   • The performance and relevance of the group will be the international FAANG steering committee

Tools

• FAANG Portal - Frontend:
  Location: https://github.com/FAANG/faang-portal-frontend
  Description: This code supports the frontend operations of the FAANG data portal
• FAANG Portal - Backend:
  Location: https://github.com/FAANG/faang-portal-backend
  Description: This code supports the backend operations of the FAANG data portal
• DCC SRA XML
  Location: https://github.com/FAANG/dcc-sra-xml
  Description: A library for building SRA XML.
• GENE-SWitCH
  Location: https://github.com/FAANG/proj-gs-iso-seq
  Description: GENE-SWitCH project Iso-Seq analysis pipeline
• FAANG Geolocation
  Location: https://github.com/FAANG/faang-gelocation
  Description: This is a series of scripts for plotting maps of FAANG members
• FAANG TAGADA
  Location: https://github.com/FAANG/analysis-TAGADA
  Description: Transcripts And Genes Assembly, Deconvolution, Analysis
• FAANG Format transcriber
  Location: https://github.com/FAANG/faang-format-transcriber
  Description: The FormatTranscribe module is designed to allow easy translating of standard formats (GTF, GFF3, Fasta), both filtering fields and mutating them based on callback functions.
• Reference Data Builder
  Location: https://github.com/FAANG/reference_data_builder
  Description: Build reference files required for genomic analysis from a gzipped fasta file and a gff file
• SRA XML
  Location: https://github.com/FAANG/sra_xml
  Description: Helper code for writing SRA XML, focusing initially on the analysis object
• Genome Signal Tracks
  Location: https://github.com/FAANG/genome-signal-tracks
  Description: This repo provides tools for creating Mappability file generation and Signal track production.