Whole genome alignment howto

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The procedure described here is for a lift over construction between two different species genomes. There is a different procedure for Same_species_lift_over_construction.

Scripts like doBlastzChainNet.pl and colleagues automate the whole process for the folks working at UCSC but don't really make it any easier to fully understand the system for an outsider, as everything is buried in hgAutomate-Perl and full of parasol statements. I'm doing a whole genome alignment in the following with bash as the only tool.

This page is based on doBlastzChainNet.pl, Conservation Track, this page which is very similar, and Angie's mental model of chains/nets. See also Blastz and Conservation_Track.

Zhenguo Zhu at PSU is also trying to understand the pipeline [1].

Thanks a lot to Angie and Hiram for answering all my questions!

Some updates (12/2009) from Angie on the pipeline.

Before you start

To understand the following you need to:

  1. Know about shell scripting. In case of doubt, use the Bash Scripting Guide as a reference.
  2. Have your own UCSC genome browser installed and running, see Learn_about_the_Browser. There is also some helpful information about UCSC's comparative genomics track data in http://www.gmod.org/wiki/index.php/GBrowse_UCSC_Plugin_Install_HOWTO.
  3. If is helpful if you have have created a UCSC browser tracks yourself, loaded it with hgLoadBed and configured it in trackDb.ra, see Learn_about_the_Browser and Adding New Tracks to a browser installation

You will need a compute cluster for bigger genomes. Depending on where you work, one of these might be free for you:

  1. Vital-IT in Switzerland, available for most European users
  2. XSede, for the USA
  3. National Grid Services in the UK


I already knew the basic file formats like bed/gff/etc, but hadn't crossed some of these yet:

  1. lav: a compact form to store genomic pairwise alignments created by Blastz, using only numbers (pos of match + identities). As of late 2009, the pipeline has replaced blastz with lastz (see http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html], but this is almost the same.
  2. psl: similar to lav, but the most compact format at UCSC to store alignments, easier to parse than lav (positions of match + identities), e.g. blat is creating this
  3. axt: a much more readable way to store *pairwise* alignments: positions + aligned sequences (It seems that you can forget about this format, it's rarely used, but the tools still contain axt... in their name although most also accept psl. )
  4. maf: an extended version of axt, *multiple* genomic alignments: assemblies + positions + aligned sequences

As you can see from the above, to convert from lav to maf we need the genomic sequences from the nib/fa files.


  1. MASKING: Both genomes have to be repeatmasked and masked Tandem Repeat Finder (trf) first (thanks to Hiram for pointing this out)
  2. ALIGNING: The two genomes are aligned with BLASTZ (we don't use blastz's own chaining, see discussion (angie)). This generates lav-files, which have to be converted to psl (lavToPsl)
  3. CHAINING: Two matching alignments next to each other are joined into one fragment if they are close enough (axtChain). As every genomic fragment can match with several others, we keep only the longest chains : first do axtSort then filter with axtBest (more info on the mailing list)
  4. NETTING: Group blocks of chained alignments into longer stretches of synteny (netChain)
  5. MAF'ING: From the synteny-files (positions), get the sequences and re-create alignments
  6. PhastCons: Using the maf-files, calculate the strength of conservation for every base, similar to a Vista- or protein Conservation plot, but applicable to multiple alignments

Outline - Notes

  • BLASTZ: The reference genome is aligned with all others with BLASTZ. That creates lav-files. They are converted to psl.
    • Angie says: Our hgdownload $db/vs$OtherDb/README.txt pages give the blastz parameters used for a given run.
    • It's a good idea to do this on a compute cluster. It took ages on my own computer. I'm European, so I got an account vital-it, anyone can apply who is working in the EU. There are national compute cluster also in the Netherlands and the UK that I know of.
  • Chains are simply better alignments: If several alignments overlap, we still don't know which the best one is. This filtering was done with axtBest before, now we use chainNet + netToAxt. (Sometimes UCSC also uses netfilter to filter out nets with a gapsize <= 12)
  • We feed the tree into multiz. Multiz will use many local alignments to generate a multiple local alignment.
 Example: A-B and A-C have been aligned with blastz...
    A aaactg  \
    B aa--tg   \     A aaa-ctg
                ->   B aa---tg
    A aaa-ctg  /     C aattt-g
    C aattt-g /
  • Multiz is not a real aligner, as it uses Blastz
  • Multiz is "a phylogenetic tree directed multiple alignment. It starts with subsets of the phylo tree with sequences that are already close to each other. As they are combined, new gaps will appear and poorly aligned paired sequences will disappear to produce a better multiple alignment at a higher scale." (thanks to Hiram, replied to me on the mailing list in 2011)
  • Multiz is not needed if you only have two species, as the chain information from blastz/lastz will contain the same information.
  • TBA is more like a real aligner. But it's too slow currently for massiv genome-wide alignments. (according to Angie) and is only used for the encode regions.
  • The only other aligner on whole genomes that I know of is SLAGAN. In theory, its output can be converted to lav but I doubt that anyone has ever tried this. SLAGAN is not related to Blastz. I have alignments for Ci/Cs made by both algorithms and they differ quite a lot, however, I've never explored the subject in detail in the end and will probably stick with Blastz

Example, step 1: Alignments with Blastz

Please note the script runLastzChain.sh: File:RunLastzChain sh.txt which encapsulates the procedures to generate the required steps for the lastz and chain operations. This script requires File:ConstructLiftFile pl.txt from the genomewiki, and partitionSequence.pl from the kent source tree.

  • I want to do a whole genome alignment of C. intestinalis V2 and C.savignyi V2. This is rather small genome (150 MB). Note that ci2 stands for Ciona intestinalis and cs2 stands for Ciona savignyi
    • Downloaded ci2 from hgdownload.cse.ucsc.edu into the directory ci2
    • Downloaded cs2 (only visible on hgwtest.cse.ucsc.edu, not on the real server nor the download server) from Ensembl into the directory cs2
  • Sometimes genomes come in one big fasta file, we want to split it into smaller ones:

  faSplit byName cs2/cs2.fa cs2/
  rm -f cs2/cs2.fa

  • The Ensembl genome cs2 does not seem to be tandem repeat masked yet, so I do:

  for i in cs2/*.fa; do trfBig $i trf/`basename $i`; done

  • Blastz seems to ignore lower case characters (took me one afternoon to figure this out), we simply convert everything to nib-format:

  for i in in ci2/* cs2/*; do faToNib $i `echo $i | sed -e s/.fa/.nib/`; done

  • Then, to blastz everything onto everything, in theory we could issue this command:

  for i in cs2/*.nib; do echo 'for j in ci2/*.nib; do blastz '$i' $j  H=2000 Y=3400 L=6000 K=2200 Q=HoxD55.q > lav/`basename '$i' .nib`-`base name $j .nib`.lav; done'; done

  • However, I better use the cluster at vital-it.ch: I rsync the nib files onto it and add a cluster instruction:

  for i in cs2/*.nib; do echo 'for j in ci2/*.nib; do bsub blastz '$i' $j  H=2000 Y=3400 L=6000 K=2200 Q=HoxD55.q > lav/`basename '$i' .nib`-`base name $j .nib`.lav; done'; done

    • In my case I have 4000 scaffolds on one genome and 400 reftigs on the other. That was still doable with the cluster.
    • However, if both genomes are spread across many more scaffolds you have to play around with the sequences, otherwise it will be millions of blastz-runs. At UCSC they first join the smaller scaffolds into one big chromsome and then run blastz on the "ChrUn"-virtual-chromosome. (this will create some false nets, going from one scaffold to another, but we don't have a choice here (hiram))

Example, step 2: Chaining

  • Convert the lav files into the more compact psl format:

  for i in *.lav; do echo $i; lavToPsl $i `basename $i .lav`.psl; done; 
  rm -f *.lav
  less chr01p.psl

  • Oups. Now, once again, I've messed up target and query. My psl-files actually look like "... chrom01 ... reftig1..." (the format is query, target). However, since I want to annotate Ci2, which is assembled into chromosomes, chrom01 should really be the target. I have to swap these fields in the current psl files and re-create new psl-files, split by the name of the target:

 cat *.psl > ../all.psl
 pslSwap ../all.psl ../all-swap.psl
 pslSplitOnTarget all-swap.psl psl/ -lump

  • Now the chaining (this is quite fast for my little ciona-genome):

 for i in psl/*.psl; do echo $i; axtChain $i ci2 cs2 chain/`basename $i .psl`.chain -linearGap=loose -psl; done

  • For the filtering of the chains, we need the size of each chromosome:

 faSize ../genome/ci2.fa -detailed > ci2.sizes
 faSize ../../cs/cs2/cioSav2.fa -detailed > cs2.sizes

  • Sort and filter the chains (more info in this post of the mailing list):

  chainMergeSort chain/*.chain > all.chain
  chainPreNet all.chain ci2.sizes cs2.sizes all.pre.chain

  • We load these chains into the browser (hm...wouldn't it be more interesting to have the complete chains in the browser?):

 hgLoadChain ci2 chainCioSav2 all.pre.chain

  • Adding a section similar to the following to trackDb.ra, running make alpha DBS=<yourdbname> ZOO= there, the track should then appear on the browser:

 track chainCioSav2
 shortLabel C. savignyi chain
 longLabel C. savignyi chain
 group compGeno
 priority 125
 visibility hide
 color 100,50,0
 altColor 255,240,200
 spectrum on
 type chain cioSav2
 otherDb cioSav2

Example, step 3: Netting

  • Then the netting itself, combine the chains into nets and add synteny information (not sure where this is displayed, probably needed for double/single-lines display of net-tracks) to them:

  chainNet all.pre.chain -minSpace=1 ci2.sizes cs2.sizes stdout /dev/null | netSyntenic stdin noClass.net

  • We need to add additional information to this nets (shown on the details page):

  netClass -noAr noClass.net ci2 cioSav2 cioSav2.net

NB: I got an error message here because of the gap.bin field in cioSav2 which does not seem to exist in lib/agpGap.c, function agpGapLoad, but is retrieved by "select * from gap order by chrom". I hacked around the problem but there shouldn't really be any error message.

  • Finally, we can load these nets into our own browser:

  hgLoadNet ci2 netCioSav2 cioSav2.net

adding something like this to trackDb.ra:

 track netCioSav2
 shortLabel C. savignyi Net
 longLabel $o_Organism ($o_date/$o_db) Alignment Net
 group compGeno
 priority 134
 visibility dense
 spectrum on
 type netAlign cioSav2 chainCioSav2
 otherDb cioSav2

Example, step 4: Maffing

  • I needs mafs for the browser as I want to display the alignments. This is also the right time to sort the alignments as they need to be sorted for downstream tools like mafsInRange (cut out only selected blocks).

 netToAxt cioSav2.net all.pre.chain ci2/ cs2/ stdout | axtSort stdin ci2-cioSav2.axt
 axtToMaf ci2-cioSav2.axt ci2.sizes cs2.sizes ci2-cioSav2.maf -tPrefix=ci2. -qPrefix=cioSav2.

  • Load the data into the brower. It needs an mysql-index to find the right position. The alignment files go into /gbdb:

 hgLoadMafSummary ci2 mafCioSav2Summary ci2-cioSav2.maf
 sudo mkdir /gbdb/ci2/mafCioSav2
 sudo cp ci2-cioSav2.maf /gbdb/ci2/mafCioSav2/mafCioSav2.maf
 hgLoadMaf ci2 mafCioSav2

Example, step 5: Phastcons

  • Phastcons doesn't seem to like big maf files that include many chromsomes, so I split the maf files by chromosome:

  mkdir maf
  mafSplit -byTarget dummy.bed maf/ ci2-cioSav2.maf

  • I take the biggest chromsome and calculate the background model from it:

  ${PHAST}/bin/phyloFit -i MAF maf/002.maf

  • Run phastCons on every maf file with this background model and some obscure parameters that phastCons needs. I'm parsing the chrosomome name here from the maf as it was lost during the mafSplitByTarget (there should be an easier way but it works):

 mkdir wig
 mkdir mostCons
 for i in maf/*.maf; do \
         x=`basename $i .maf`;
         ~/bio/phastCons/bin/phastCons --target-coverage 0.25 --expected-length 12 \
          --rho 0.4 --msa-format MAF $i phyloFit.mod \
          --seqname `cat $i | head -n 3  | tail -n 1 | tr -s ' ' | cut -f 2 -d ' ' | cut -d. -f2`
          --most-conserved mostCons/$x.bed > wig/$x.wig; \

This took 7 minutes for a maf file of 113 MB

Q: How can I check if these parameters are "good"? Use CDS overlap?

  • Load the wiggle files into the browser:

 cat wig/*.wig > ../ci2-cioSav2.pp
 wigEncode ci2-cioSav2.pp ci2-cioSav2.wig ci2-cioSav2.wib
 sudo mkdir /gbdb/ci2/wib/
 sudo cp ci2-cioSav2.wib /gbdb/ci2/wib/
 hgLoadWiggle  -pathPrefix=/gbdb/ci2/wib ci2 phastCons ci2-cioSav2.wig

  • Load the "most Conserved" regions into the browser:

 cat mostCons/*.bed > mostCons.bed
 hgLoadBed ci2 mostConserved mostCons.bed

  • ... add something like this entry in trackDb.ra:

 track mafCioSav2
 shortLabel Conservation
 longLabel Blastz/Phastcons conservation C. savignyi
 group compGeno
 visibility full
 type wigmaf 0.0 1.0
 speciesOrder ci2 cioSav2
 wiggle phastCons
 viewLimits 0:1
 autoScale off
 maxHeightPixels 50:50:11

  • Refreshing my trackDb (make ...) will then display the track


  • The original authors already wrote similar tools: Multiz contains a tool that converts lav2maf directly and UCSC includes one with lavToMaf. However, we don't care about fragments that match two times. For a whole genome, you really want "chains" of best-matching fragments, therefore we don't use these tools.
  • For the records: In the UCSC source tree, the AXT format started in the mouseStuff directory and MAF started in the ratStuff directory. There is an older tool called *axtBest* but Angies says: "axtBest is ancient history. It has been replaced by the chaining and netting process, which does a better job of finding the "best" alignment to cover a given region."
  • Why do mafs include the chrosome sizes? I don't know.
  • GERP is an alternative for phastCons from the Sidow lab and used by the Ensembl browser.
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