References

References¶

The reference sequences comprises of the host genome and the viral genomes.

Fasta¶

hg38 and mm39 genome builds are chosen to represent hosts. Ribosomal sequences (45S, 5S) are downloaded from NCBI. hg38 and mm39 were masked for rRNA sequence and 45S and 5S sequences from NCBI are appended as separate chromosomes. The following viral sequences were appended to the rRNA masked hg38 reference:

HOSTS:
  * hg38          [Human]
  * mm39          [Mouse]

ADDITIVES:
  * ERCC          [External RNA Control Consortium sequences]
  * BAC16Insert   [insert from rKSHV.219-derived BAC clone of the full-length KSHV genome]

VIRUSES:
  * NC_007605.1   [Human gammaherpesvirus 4 (Epstein-Barr virus)]
  * NC_006273.2   [Human betaherpesvirus 5 (Cytomegalovirus )]
  * NC_001664.4   [Human betaherpesvirus 6A (HHV-6A)]
  * NC_000898.1   [Human betaherpesvirus 6B (HHV-6B)]
  * NC_001716.2   [Human betaherpesvirus 7 (HHV-7)]
  * NC_009333.1   [Human gammaherpesvirus 8 (KSHV)]
  * NC_045512.2   [Severe acute respiratory syndrome(SARS)-related coronavirus]
  * MN485971.1    [HIV from Belgium]
  * NC_001806.2   [Human alphaherpesvirus 1 (Herpes simplex virus type 1)](strain 17) (HSV-1)]
  * KT899744.1    [HSV-1 strain KOS]
  * MH636806.1    [MHV68 (Murine herpesvirus 68 strain WUMS)]

Location: The entire resource bundle is available at /data/CCBR_Pipeliner/db/PipeDB/charlie/fastas_gtfs on BIOWULF. This location also have additional bash scripts required for aggregating annotations and building indices required by different aligners.

When -m=dryrun is run for the first time after initialization (-m=init), the appropriate host+additives+viruses fasta and gtf files are created on the fly, which are then used to build aligner reference indexes automatically.