This directory contains alignments of the following assemblies:

  - target/reference: White throated tinamou
    (tinGut2, Aug 2014 (ASM70537v2/tinGut2),
    BGI GCA_000705375.2)

  - query: Chicken
    (galGal6, Mar. 2018 (GRCg6a/galGal6),
    Genome Reference Consortium)

Files included in this directory:

  - md5sum.txt: md5sum checksums for the files in this directory

  - tinGut2.galGal6.all.chain.gz: chained lastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - tinGut2.galGal6.net.gz: "net" file that describes rearrangements between
    the species and the best Chicken match to any part of the
    White throated tinamou genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - tinGut2.galGal6.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the White throated tinamou genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in http://genome.ucsc.edu/goldenPath/help/axt.html .

  - tinGut2.galGal6.synNet.maf.gz - filtered net file for syntenic alignments
               only, in MAF format, see also, description of MAF format:
               http://genome.ucsc.edu/FAQ/FAQformat.html#format5

  - tinGut2.galGal6.syn.net.gz - filtered net file for syntenic alignments only

  - reciprocalBest/ directory, contains reciprocal-best netted chains
    for tinGut2-galGal6

The chainSwap program was used to translate galGal6-referenced chained lastz
alignments to tinGut2 into tinGut2-referenced chains aligned to galGal6.  See
the download directory goldenPath/galGal6/vsTinGut2/README.txt for more
information about the galGal6-referenced lastz and chaining process.

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after lastz were written by Jim Kent at UCSC.

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If you plan to download a large file or multiple files from this directory,
we recommend you use ftp rather than downloading the files via our website.
To do so, ftp to hgdownload.soe.ucsc.edu, then go to the directory
goldenPath/tinGut2/vsGalGal6/. To download multiple files, use the "mget"
command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all files in the current directory)

All files in this directory are freely available for public use.

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References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence
alignments. Pac Symp Biocomput.  2002:115-26.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep
30;100(20):11484-9.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome
Res. 2003 Jan;13(1):103-7.