The "analysis set" is a version of the genome prepared for next-gen
sequencing read alignment. We are making available versions of the NCBI
files here converted into UCSC formats. For a full description of 
the "analysis set" concept, see NCBI's README file:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

Below are the original UCSC analysisSet files.
These files are no longer updated. For the latest analysis
set see the FTP NCBI directory at the address above. 

Files included in this directory:

hg38.analysisSet.2bit - analysis set sequence
hg38.analysisSet.fa.gz - analysis set sequence
hg38.analysisSet.chroms.tar.gz - analysis set sequence one file per chromosome
    The analysis set sequence is masked as mentioned in ../README.txt,
    repeats from RepeatMasker and Tandem Repeats Finder
    (with period of 12 or less) are shown in lower case;
    non-repeating sequence is shown in upper case.
    The sequences in the file are otherwise identical to the NCBI file
    GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

hg38.fullAnalysisSet.2bit - all of the sequence from the above set,
    plus all of the alt-scaffolds from the GRCh38 ALT_REF_LOCI_* assembly units.
hg38.fullAnalysisSet.chroms.tar.gz - all of the sequence from the above set,
    plus all of the alt-scaffolds from the GRCh38 ALT_REF_LOCI_* assembly units.
    The analysis set sequence is masked as mentioned in ../README.txt,
    repeats from RepeatMasker and Tandem Repeats Finder
    (with period of 12 or less) are shown in lower case;
    non-repeating sequence is shown in upper case.

md5sum.txt - checksums of files in this directory

      Name                               Last modified      Size  Description
      Parent Directory                                        -   
      hg38.analysisSet.2bit              2014-01-27 10:40  770M  
      hg38.analysisSet.chroms.tar.gz     2014-01-27 11:02  905M  
      hg38.fullAnalysisSet.2bit          2014-03-18 13:23  797M  
      hg38.fullAnalysisSet.chroms.tar.gz 2014-03-18 13:41  936M  
      hg38.analysisSet.fa.gz             2021-09-01 00:30  905M  
      md5sum.txt                         2021-09-01 01:00  307