Reference Data

Reference Data

Reference data used by modules.

AlphaFold 3

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence.

  • Date: Dec 1, 2024
  • Method: /app/software/AlphaFold3/alphafold3/fetch_databases.sh
  • Version: 3.0.0
  • DB_DIR=/hpc/reference/alphafold3/

Directory List

mmcif_files/  # Directory containing ~200k PDB mmCIF files.
bfd-first_non_consensus_sequences.fasta
mgy_clusters_2022_05.fa
nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta
pdb_seqres_2022_09_28.fasta
rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta
rnacentral_active_seq_id_90_cov_80_linclust.fasta
uniprot_all_2021_04.fa
uniref90_2022_05.fa

Ensembl Data

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

/shared/biodata/ngs/Reference/Genomes/Homo_sapiens/Ensembl-110

10X Genomics

The Hutch has serveral packages from 10X Genomoics.

  • Cell Ranger
  • Cellranger ATAC
  • Cell Ranger ARC
  • Space Ranger

Refernce data for 10X Genomics tools is located

/shared/biodata/ngs/Reference/10X`

Kraken2

Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.

/shared/biodata/ngs/Reference/Kraken2
/shared/biodata/microbiome/kraken2

STAR2

STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Modules: STAR/2.7.10b-GCC-12.2.0

/shared/biodata/ngs/Reference/Genomes/Homo_sapiens/GRCh38/Sequence/STAR2Index

AlphaFold 2

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence.

/shared/biodata/ngs/Reference/protein/

CHOPCHOP

CHOPCHOP (version 3) is a tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1, CRISPR/Cas13 or NICKASE/TALEN-directed mutagenesis.

/shared/biodata/ngs/Reference/chopchop

gatk (Broad Institute) Funcotator Data

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

/shared/biodata/ngs/Reference/Funcotator

Bowtie2 Index data

/shared/biodata/ngs/Reference/Genomes/Drosophila_melanogaster/UCSC/BDGP6_dm6/Sequence/Bowtie2Index

Oncotator

/shared/biodata/ngs/Reference/Oncotator

PCGR - Personal Cancer Genome Reporter

/shared/biodata/ngs/Reference/pcgr/data

RSeQC (Picard-Style) Interval Files

/shared/biodata/ngs/Reference/RNASeQC/hg38_rRNA_intervals.list

SnpEff

/shared/biodata/ngs/Reference/snpEff

tcrdist3

tcrdist3 is an open-source python package that enables a broad array of T cell receptor sequence analyses. There are many other applications for analyzing TCR data; DeepTCR, clusTCR, pubtcrs.

/shared/biodata/ngs/Reference/tcrdist