If you have an idea for a new feature – send us your request. You can see all planned features and requests on the project board. Currently, we plan to download all primary and alternative ToL assemblies, as well as non-ToL (VGP, Lepidoptera, and requests) assemblies, and run the analysis pipelines only on the primary assemblies. Let us know if some analyses would be useful to have on the other assemblies too.

INSDC Download

sanger-tol/insdcdownload downloads assemblies from INSDC into a Tree of Life directory structure. This pipeline is run for all primary and alternative ToL assemblies, as well as non-ToL (VGP, Lepidoptera, and requests) assemblies.

Current features:

  • Download genome from NCBI as Fasta.
  • Put the unmasked version under assembly/release/ and the masked version under analysis/.
  • Build samtools faidx and dict indices on the genome assemblies.
  • Create BED file with the coordinates of the masked region.
  • Compress and index the BED file with bgzip and tabix.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps

If you have an idea for a new feature – send us your request. You can see all planned features and requests on the project board.

Ensembl Repeat Download

sanger-tol/ensemblrepeatdownload downloads repeat annotations from Ensembl into a Tree of Life directory structure. This pipeline is run for all primary and alternative ToL assemblies, as well as non-ToL (VGP, Lepidoptera, and requests) assemblies.

 Current features:

  • Download the masked FASTA file from Ensembl.
  • Extract the coordinates of the masked regions into a BED file.
  • Compress and index the BED file with bgzip and tabix.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps

If you have an idea for a new feature – send us your request. You can see all planned features and requests on the project board.

Ensembl Gene Download

sanger-tol/ensemblgenedownload downloads gene annotations from Ensembl into the Tree of Life directory structure. This pipeline is run for all primary and alternative ToL assemblies, as well as non-ToL (VGP, Lepidoptera, and requests) assemblies.

Current features:

  • Download from Ensembl gene annotation in GFF3 format.
  • Download from Ensembl gene sequences in FASTA format.
  • Compress and index all sequences files with bgzip, samtools faidx, and samtools dict.
  • Compress and index the annotation files with bgzip and tabix.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps

If you have an idea for a new feature – send us your request. You can see all planned features and requests on the project board.

Sequence Composition

sanger-tol/sequencecomposition extracts statistics from a genome about its sequence composition. This pipeline is run for all primary ToL assemblies.

Current features:

  • Run fasta_windows on the genome FASTA file.
  • Extract single-statistics bedGraph files from the multi-statistics outputs.
  • Compress and index all bedGraph and TSV files with bgzip and tabix.

Planned features:

Potential features:

Only if there is an actual demand ! Use the form below to indicate interest.

  • Import features from the GDA (Genome Decomposition Analysis) pipeline, for instance:
    • Low complexity repeats from Dustmasker
    • Inverted repeats from einverted
    • LTR retrotransposons from LTRharvest and LTRdigest
    • Tandem repeats from trf
    • Mappability track
    • Telomeric repeat annotation (tool to be confirmed)
    • Centromeric repeat annotation (tool to be confirmed)

If you have an idea for a new feature or would like this pipeline to run on other assemblies – send us your request. You can see all planned features and requests on the project board.

Read Mapping

sanger-tol/readmapping aligns reads generated using Illumina, HiC, PacBio and Nanopore technologies against a genome assembly. This pipeline is run for all primary ToL assemblies.

Current features:

  • Align short read data (HiC and Illumina) against the genome with bwamem2 mem
  • Mark duplicates for short read alignment with samtools.
  • Filter PacBio raw read data using vector database.
  • Align long read data (ONT, PacBio CCS and PacBio CLR) against the genome with minimap align.
  • Merge all alignment files at the individual level and convert to CRAM format.
  • Calculate statistics for all alignment files using samtools stats, flagstat, and idxstats.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps
  • Add calculation for PacBio filtered data percentage
  • Add support for Pacbio ULI reads
  • Add support for RNAseq data
  • Implement chunking to speed up alignment for all technologies
  • Include additional metadata in aligned file headers
  • Support compression with crumble for aligned files
  • Support multiple output options – BAM, compressed BAM, CRAM, compressed CRAM

If you have an idea for a new feature or would like this pipeline to run on other assemblies – send us your request. You can see all planned features and requests on the project board.

Variant Calling

sanger-tol/variantcalling calls (short) variants on PacBio data using DeepVariant. This pipeline is run for all primary ToL assemblies.

Current features:

  • Calls variants using DeepVariant for PacBio long read data.
  • Speed improvements made by splitting the genome before calling variants.
  • Outputs both VCF and GVCF formats.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps
  • Add calculation for heterozygosity, flag for homozygous alternatives, and InDel size distribution
  • Create bedGraph for distribution of heterozygous sites across genome
  • Add support for creating indices for aligned reads and the genome
  • Add support for combining multiple libraries from the same sample
  • Add support to map PacBio reads before calling variants
  • Add structural variation detection
  • Add variant calling for short read data with FreeBayes
  • Add optional read mapping subworkflow

If you have an idea for a new feature or would like this pipeline to run on other assemblies – send us your request. You can see all planned features and requests on the project board.

BlobToolKit

sanger-tol/blobtoolkit is used to identify and analyse non-target DNA for eukaryotic genomes. This pipeline will be run for all primary ToL assemblies after 1.0.0 release. Currently, the Snakemake version is used in production.

Current features:

  • Calculate sequence statistics in 1kb windows for each contig.
  • Count BUSCOs in 1kb windows for each contig using specific and basal lineages.
  • Calculate coverage in 1kb windows using blobtk depth.
  • Aggregate 1kb values into windows of fixed proportion (10%, 1% of contig length) and fixed length (100kb, 1Mb).
  • Diamond blastp search of BUSCO gene models for basal lineages (archaea_odb10, bacteria_odb10 and eukaryota_odb10) against the UniProt reference proteomes.
  • Import analysis results into a BlobDir dataset.
  • BlobDir validation and static image generation.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps
  • Improved BlobDir validation
  • Improved generation of the summary Yaml file
  • Diamond blastx search of assembly contigs against the UniProt reference proteomes
  • NCBI blastn search of assembly contigs with no Diamond blastx match against the NCBI nt database
  • Add optional read mapping subworkflow

If you have an idea for a new feature or would like this pipeline to run on other assemblies – send us your request. You can see all planned features and requests on the project board.

Genome Note

sanger-tol/genomenote generates all the data (tables and figures) used in genome note publications. These include (1) assembly information, statistics and chromosome details, (2) PacBio consensus quality and k-mer completeness, and (3) HiC contact maps and mapping statistics. This pipeline is run for all primary ToL assemblies.

Current features:

  • Create HiC contact map and chromosomal grid using Cooler.
  • Create summary table using (1) assembly information, statistics and chromosome details from NCBI datasets, (2) genome completeness from BUSCO, (3) consensus quality and k-mer completeness from MerquryFK, and (4) HiC primary mapped percentage from samtools flagstat.

Planned features:

  • Update pipeline template
  • Update samplesheet validation steps
  • Improve genome metadata fetching and processing
  • Combine results and metadata with template Word document
  • Add optional read mapping subworkflow

If you have an idea for a new feature or would like this pipeline to run on other assemblies – send us your request. You can see all planned features and requests on the project board.