IGENOMES

Section: iGenomes - reference sequences & annotation files (7)
Last updated: Wed 10 Jan 16:53:42 GMT 2024
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DEPRECATION NOTICE

This CCB documentation has been superseded by our new website: https://lumin.imm.ox.ac.uk

OVERVIEW

iGenomes is a collection of reference sequences and annotation files for commonly analyzed organisms. The files were originally generated by Illumina. The files have been downloaded from Ensembl, NCBI, or UCSC, and chromosome names have been changed to be simple and consistent with their download source.

On the CCB servers these files can be found at:

: /databank/igenomes/

The Ensembl and UCSC annotation and sequence files for the following organisms are available under these directories:

Human        /databank/igenomes/Homo_sapiens/
Mouse        /databank/igenomes/Mus_musculus/
Rat          /databank/igenomes/Rattus_norvegicus/
Zebrafish    /databank/igenomes/Danio_rerio/
Drosophila   /databank/igenomes/Drosophila_melanogaster/
Chicken      /databank/igenomes/Gallus_gallus/
Pig          /databank/igenomes/Sus_scrofa/
Chimpanzee   /databank/igenomes/Pan_troglodytes/

In these directories you will find sub-directories for Ensembl and UCSC annotation and sequence for different builds, for example:

/databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

Indices for Bowtie, Bowtie2 & BWA, and fastq format files of sequence are all in the Sequence directory:

/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex

Annotation files eg gtf files can be found in the Annotation directory:

: /databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf

GETTING HELP

You can email the CCB team using the email address help@imm.ox.ac.uk. Using this address ensures your email is logged and assigned a tracking number, and will go to all the core team, which means the appropriate person or people will be able to pick it up.

COPYRIGHT

This text is copyright University of Oxford and MRC and may not be reproduced or redistributed without permission.

AUTHOR

Duncan Tooke <duncan.tooke@imm.ox.ac.uk>