The "analysis set" is a version of the genome prepared for next-gen
sequencing read alignment. It contains no alternate sequences, no 
patches, fixes or haplotypes, only the main chromosomes. For more 
information, see https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

The files here come from NCBI, and were converted into UCSC formats. 
The files below are the original 2014 release from NCBI, without decoys
or alt-aware BWA files.
For a full description of the "analysis set" concept, see NCBI's README file:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

These files are no longer updated.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