This directory contains alignments of the following assemblies: - target/reference: Human (hg38, Dec. 2013 (GRCh38/hg38), GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) - query: human (GCA_018505855.1_HG02055.alt.pat.f1_v2, 2021-05-26, UCSC Genomics Institute) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - hg38.GCA_018505855.1.all.chain.gz: chained lastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - hg38.GCA_018505855.1.net.gz: "net" file that describes rearrangements between the species and the best human match to any part of the Human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - hg38.GCA_018505855.1.net.axt.gz: chained and netted alignments, i.e. the best chains in the Human 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 . - hg38.GCA_018505855.1.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 - hg38.GCA_018505855.1.syn.net.gz - filtered net file for syntenic alignments only - reciprocalBest/ directory, contains reciprocal-best netted chains for hg38-GCA_018505855.1 The hg38 and GCA_018505855.1_HG02055.alt.pat.f1_v2 assemblies were aligned by the lastz alignment program, which is available from Webb Miller's lab at Penn State University (http://www.bx.psu.edu/miller_lab/). Any hg38 sequences larger than 20,010,000 bases were split into chunks of 20,010,000 bases overlapping by 10,000 bases for alignment. A similar process was followed for GCA_018505855.1, with chunks of 20,000,000 overlapping by 0. Following alignment, the coordinates of the chunk alignments were corrected by the blastz-normalizeLav script written by Scott Schwartz of Penn State. The lastz scoring matrix (Q parameter) used was: A C G T A 90 -330 -236 -356 C -330 100 -318 -236 G -236 -318 100 -330 T -356 -236 -330 90 with a gap open penalty of O=600 and a gap extension penalty of E=150. The minimum score for an alignment to be kept was K=4500 for the first pass and L=3000 for the second pass, which restricted the search space to the regions between two alignments found in the first pass. The minimum score for alignments to be interpolated between was H=2000. Other lastz parameters specifically set for this species pair: E=150 M=254 O=600 T=2 Y=15000 The .lav format lastz output was translated to the .psl format with lavToPsl, then chained by the axtChain program. Chain minimum score: 5000, and linearGap matrix of (medium): tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 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. ---------------------------------------------------------------- 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/hg38/vsGCA_018505855.1/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all files in the current directory) All files in this directory are freely available for public use. -------------------------------------------------------------------- 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.