Hi everybody,

can anyone guide me from where to download the hs37d5.fa genome merged with phiX genome?

I have downloaded few BAM files containing the tag in header section @SQ SN:PhiX LN:6386 together with other hs37d5/fa  contigs. I am looking for which version of the reference sequence was used for these files.

any help would be appreciated!


Regards

(Note: I am aware of phiX genome is used perhaps a control in illumina sequencing.)
If you want *exactly* the MPI-EVA version (which includes a circularised phiX and extended reference mtDNA) the construction is similar to the reference used by the 1000 Genomes Project (compare ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/),
with minor changes. It's made as follows :

1  Download individual chrs from ensembl ftp (just like 1000g)
   ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/


2a Download the newer version of the mitochondrion (NC_012920, just like 1000g)
   http://www.ncbi.nlm.nih.gov/nuccore/251831106

2b Copy the first 1000bp of the mitochondrion onto its end.  The resulting sequence is named "MT".


3  Download the concatenated decoy sequences from 1000 Genomes:
   ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5cs.fa.gz

Also compare their READMEs:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.slides.pdf


4  Download the Human herpes virus (NC_007605, aka EBV) from NCBI, just like 1000g.  The sequence is then named "NC_007605".
   http://www.ncbi.nlm.nih.gov/nuccore/NC_007605


5a Download phiX-174 reference (NC_001422).
   http://www.ncbi.nlm.nih.gov/nuccore/NC_001422

5b Copy the first 1000bp of phiX onto its end, name the result "phiX".


6  Create a reference (whole_genome.fa) with chrs 1-22, X, Y, extended
   NC_012920 MT, the non-chromosomal supercontigs, the
   NC_007605 EBV, the decoy sequences (hs37d5), extended phiX.
   The order is chosen to match 1000 Genomes (plus phiX), see their fai file:
   ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz.fai

Note that two sequences (MT, PhiX) are circular and have been extended to
facilate alignment.  The correct incantation to wrap these alignments to their
correct length is

      bam-rewrap MT:16569 phiX:5386

or

      bam-rmdup -z MT:16569 -z phiX:5386