Comparative genome data for the manuscript
"The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly"
by Roscito et al. 2018.


The directory contains
- tegu.HLtupMer6.2bit					Tegu v2 assembly in 2bit format
- tegu.HLtupMer6.fasta.gz				Tegu v2 assembly in fasta format
- tegu.HLtupMer3.2bit                                   Tegu v1 assembly in 2bit format
- tegu.HLtupMer3.fasta.gz				Tegu v1 assembly in fasta format

- multiz_17way.maf.gz 					Multiple alignment of 17 amniote species, with tegu assembly v2 (HLtupMer6) as reference.
- tree.mod                                              Phylogenetic tree with neutral branch lengths.

- tegu.GERPElements.bed					Conserved elemented determined by GERP, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.PhastConsElements.bed         			Conserved elements determined by PhastCons, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.conservedElements.bed				Conserved elements after merging PhastCons and GERP elements, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.CNEs.bed						Conserved non-exonic elements (no overlap with exons of annotated genes), in tegu assembly v2 (HLtupMer6) coordinates
- tegu.CNEs.reptileSpecific.bed				CNEs that are reptile-specific, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.CNEs.reptileSpecific.transposonDerived.bed	CNEs that are reptile-specific and overlap transposons, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.genes.gp						Gene annotation, genePred format, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.genes.gff3					Gene annotation, gff3 format, in tegu assembly v2 (HLtupMer6) coordinates
- tegu.genes.proteins.fasta				Protein sequences
- tegu.genes.transcripts.fasta				cDNA sequences 

- UCEs.fasta						197 non-exonic Ultra-Conserved Elements, used to assess assembly completeness
- CNEs.fasta						493 deeply-conserved non-exonic elements, used to assess assembly completeness 

- opticalMap_thinkmate.tgz				Optical map data

- assemblyHub						Directory containing all files for UCSC assembly hub

The assemblies included in the multiple alignment are:
HLtupMer6  Tegu
anoCar2    Green_anole_lizard
HLpogVit2  Dragon_lizard
HLophGra1  Asian_glass_lizard
HLvipBer1  Common_viper
HLproMuc1  Brown_spotted_pitviper
HLthaSir1  Common_garter_snake
boaCon1    Boa_constrictor
pytBiv1    Burmese_python
HLgekJap1  Schlegels_japanese_gecko
galGal5    Chicken
melUnd1    Budgerigar
allMis1    Alligator
cheMyd1    Green_seaturtle
pelSin1    Chinese_softshell_turtle
hg38       Human
mm10       Mouse