DOI: 10.5061/dryad.fttdz0913
title: Hyalinobatrachium fleischmanni genome sequencing and assembly

description: This sample is from a male bred in captivity in the USA, collected and
 coordinated by Lauren O'Connell at Stanford University, and used to
 generate a high-quality reference genome for a project on glassfrog
 transparency. Sequencing and genome assembly were conducted by Dovetail
 Genomics in Santa Cruz, California.
description: # Hyalinobatrachium fleischmanni Genome sequencing and assembly ##
 Description of files **The purpose of this project is to determine the
 underlying neural, genetic and physiological mechanisms that coordinate
 osmoregulation and parental care. Previously, there were no publicly
 available genomes for glassfrogs.** **Files included in set:**  .txt files
 include h.batrachium scaffold data, tables describing breaks in the input
 scaffolds, describes gaps in final assembly. .pdf files include quality
 reports from Dovetail.\ .bam files are binary alignment maps (in parts),
 an indexable representation of nucleotide sequences alignments,using the
 Chicago method and HiRiSe software to generate scaffolds. refer to
 manifest.txt file for more information. | **file name** | **library
 source** | **library selection** | **library strategy** | **library
 layout** | **platform** | **instrument model** | **design description** |
 **file type** | |
 :---------------------------------------------------------------------- |
 :----------------- | :-------------------- | :------------------- |
 :----------------- | :----------- | :------------------- |
 :--------------------- | :------------ | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx.fasta.gz | GENOMIC |
 RANDOM | WGS | single | ILLUMINA | Illumina HiSeq X | Other | fastq | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx\_filtered.fasta |
 GENOMIC | RANDOM | WGS | single | ILLUMINA | Illumina HiSeq X | Other |
 fastq | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx\_filtered.fasta.fai |
 GENOMIC | RANDOM | WGS | single | ILLUMINA | Illumina HiSeq X | Other |
 fastq | | chicago\_lib\_001.sorted.md.bam | GENOMIC | RANDOM | OTHER |
 single | ILLUMINA | Illumina HiSeq X | Chicago | bam | |
 chicago\_lib\_002.sorted.md.bam | GENOMIC | RANDOM | OTHER | single |
 ILLUMINA | Illumina HiSeq X | Chicago | bam | |
 chicago\_lib\_003.sorted.md.bam | GENOMIC | RANDOM | OTHER | single |
 ILLUMINA | Illumina HiSeq X | Chicago | bam | |
 hyalinobatrachium\_fleischmanni\_01Nov2019\_jncQJ.fasta.gz | GENOMIC |
 RANDOM | RNA-Seq | single | ILLUMINA | Illumina HiSeq X | Other | fastq |
 | hyalinobatrachium\_fleischmanni\_01Nov2019\_jncQJ\_filtered.fasta |
 GENOMIC | RANDOM | RNA-Seq | single | ILLUMINA | Illumina HiSeq X | Other
 | fastq | | hirise\_lib\_001.sorted.md.bam | GENOMIC | RANDOM | Hi-C |
 single | ILLUMINA | Illumina HiSeq X | HiRiSE | bam | |
 hirise\_lib\_002.sorted.md.bam | GENOMIC | RANDOM | Hi-C | single |
 ILLUMINA | Illumina HiSeq X | HiRiSE | bam | |
 hirise\_lib\_003.sorted.md.bam | GENOMIC | RANDOM | Hi-C | single |
 ILLUMINA | Illumina HiSeq X | HiRiSE | bam | |
 hirise\_lib\_004.sorted.md.bam | GENOMIC | RANDOM | Hi-C | single |
 ILLUMINA | Illumina HiSeq X | HiRiSE | bam | |
 hirise\_lib\_005.sorted.md.bam | GENOMIC | RANDOM | Hi-C | single |
 ILLUMINA | Illumina HiSeq X | HiRiSE | bam | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx.table.txt | | | | | | |
 | text | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx.gapclosing\_table.txt |
 | | | | | | text | | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx.report.pdf | | | | | | |
 | pdf | |
 hyalinobatrachium\_fleischmanni\_08Aug2019\_WFrIx.input\_breaks.txt | | |
 | | | | | text | |
 hyalinobatrachium\_fleischmanni\_01Nov2019\_jncQJ.report.pdf | | | | | | |
 | pdf | | hyalinobatrachium\_fleischmanni\_01Nov2019\_jncQJ.table.txt | |
 | | | | | | text | |
 hyalinobatrachium\_fleischmanni\_01Nov2019\_jncQJ.input\_breaks.txt | | |
 | | | | | text | | list\_chicago\_to\_filter.txt | | | | | | | | text | |
 list\_final\_HiC\_to\_filter.txt | | | | | | | | text | | manifest.txt | |
 | | | | | | text |