Hyalinobatrachium fleischmanni genome sequencing and assembly
Data files
Apr 15, 2024 version files 251.13 GB
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chicago_lib_001.sorted.md.bam
29.34 GB
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chicago_lib_002.sorted.md.bam
32.37 GB
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chicago_lib_003.sorted.md.bam
29 GB
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hirise_lib_001.sorted.md.bam
28.71 GB
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hirise_lib_002.sorted.md.bam
29.07 GB
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hirise_lib_003.sorted.md.bam
37.83 GB
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hirise_lib_004.sorted.md.bam
28.10 GB
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hirise_lib_005.sorted.md.bam
26.81 GB
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hyalinobatrachium_fleischmanni_01Nov2019_jncQJ_filtered.fasta
3.58 GB
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hyalinobatrachium_fleischmanni_01Nov2019_jncQJ.fasta.gz
1.06 GB
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hyalinobatrachium_fleischmanni_01Nov2019_jncQJ.input_breaks.txt
2.99 KB
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hyalinobatrachium_fleischmanni_01Nov2019_jncQJ.report.pdf
603.76 KB
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hyalinobatrachium_fleischmanni_01Nov2019_jncQJ.table.txt
16.70 MB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx_filtered.fasta
4.12 GB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx_filtered.fasta.fai
12.17 MB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.fasta.gz
1.09 GB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.gapclosing_table.txt
3.92 MB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.input_breaks.txt
167.86 KB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.report.pdf
236.10 KB
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hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.table.txt
24.94 MB
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list_chicago_to_filter.txt
3.90 KB
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list_final_HiC_to_filter.txt
3.96 KB
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manifest.txt
3.39 KB
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README.md
6.86 KB
Abstract
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 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 | ||||||||
hyalinobatrachium_fleischmanni_08Aug2019_WFrIx.input_breaks.txt | text | |||||||
hyalinobatrachium_fleischmanni_01Nov2019_jncQJ.report.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 |