Difference between revisions of "Seagrasses"
Philippbayer (talk | contribs) |
Philippbayer (talk | contribs) |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
This page collects assemblies, annotations, and supplementary data for the <i>Amphibolis antarctica</i> and <i>Posidonia australis</i> genome assemblies. | This page collects assemblies, annotations, and supplementary data for the <i>Amphibolis antarctica</i> and <i>Posidonia australis</i> genome assemblies. | ||
| − | The raw reads are deposited in the SRA under BioProject PRJNA835502 | + | The raw reads and assemblies are deposited in the SRA under BioProject PRJNA835502 |
== <i>Posidonia australis</i> == | == <i>Posidonia australis</i> == | ||
| Line 11: | Line 11: | ||
MAKER annotation: | MAKER annotation: | ||
| − | GFF of all evidence: [ | + | GFF of all evidence: [https://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.gff.gz P_australis_genome_bigger1kbp.all.gff.gz] |
| − | |||
| − | Proteins (fasta): [ | + | GFF of gene models only: [https://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.gene_models.gff.gz P_australis_genome_bigger1kbp.all.gene_models.gff.gz] |
| − | Transcripts/CDS (fasta): [ | + | |
| + | |||
| + | Proteins (fasta): [https://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.maker.proteins.fasta.gz P_australis_genome_bigger1kbp.all.maker.proteins.fasta.gz] | ||
| + | |||
| + | Transcripts/CDS (fasta): [https://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.maker.transcripts.fasta.gz P_australis_genome_bigger1kbp.all.maker.transcripts.fasta.gz] | ||
| + | |||
| + | == <i>Amphibolis antarctica</i> == | ||
| + | |||
| + | Draft genome assembly: | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.fasta.gz A_antarctica_genome_bigger1kbp.fasta.gz] | ||
| + | |||
| + | MAKER annotation: | ||
| + | |||
| + | GFF of all evidence: [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.gff.gz A_antarctica_genome_bigger1kbp.all.gff.gz] | ||
| + | |||
| + | GFF of gene models only: [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.gene_models.gff.gz A_antarctica_genome_bigger1kbp.all.gene_models.gff.gz] | ||
| + | |||
| + | |||
| + | Proteins (fasta): [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.maker.proteins.fasta.gz A_antarctica_genome_bigger1kbp.all.maker.proteins.fasta.gz] | ||
| + | |||
| + | Transcripts/CDS (fasta): [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.maker.transcripts.fasta.gz A_antarctica_genome_bigger1kbp.all.maker.transcripts.fasta.gz] | ||
| + | |||
| + | |||
| + | == Chloroplast assemblies and annotations == | ||
| + | |||
| + | Annotations (gff): | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/A.antarctica.gff3.gz A. antarctica] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/P.australis.gff3.gz P. australis] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Z.marina.gff3.gz Z. marina] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Z.muelleri.gff3.gz Z. muelleri] | ||
| + | |||
| + | Annotations (genbank): | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/A.antarctica.gbff.gz A. antarctica] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/P.australis.gbff.gz P. australis] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Z.marina.gbff.gz Z. marina] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Z.muelleri.gbff.gz Z. muelleri] | ||
| + | |||
| + | Assemblies | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/amphibolis_chloroplast.fasta.gz A. antarctica] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/posidonia_chloroplast.fasta.gz P. australis] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/zmarina_chloroplast.fasta.gz Z. marina] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/zmuelleri_chloroplast.fasta.gz Z. muelleri] | ||
| + | |||
| + | == EDTA results == | ||
| + | |||
| + | These are EDTA TE libraries, annotated using TEfinder using rexdb-plant. I renamed the TE names, if TEfinder had no hit, I used the EDTA name. | ||
| + | |||
| + | For example, this is the TEfinder output: | ||
| + | |||
| + | >TE_00000000#Unknown TE_00000000#DNA/DTC | ||
| + | |||
| + | Saying that TEfinder does not know the class, but EDTA has it under DNA/DTC based on the tool that predicted it. | ||
| + | |||
| + | I replaced these cases with a small script, this is the final name in the files below in cases where TEfinder could not find a class: | ||
| + | |||
| + | >TE_00000000#DNA/DTC TE_00000000#DNA/DTC | ||
| + | |||
| + | <i>Amphibolis antarctica</i>: [https://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz A_antarctica_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz] | ||
| + | |||
| + | <i>Posidonia australis</i>: [https://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz P_australis_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz] | ||
| + | |||
| + | <i>Zostera muelleri</i>: [https://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.big1k.merged_scaffolds.renamed.fa.mod.EDTA.TElib.fa.rexdb.cls.renamed.lib.fa.gz Zmu_v1_scaffolds.big1k.merged_scaffolds.renamed.fa.mod.EDTA.TElib.fa.rexdb.cls.renamed.lib.fa.gz ] | ||
| + | |||
| + | <i>Zostera marina</i>: [https://appliedbioinformatics.com.au/download/Zostera_marina.mainGenome.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz Zostera_marina.mainGenome.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz ] | ||
Latest revision as of 03:28, 15 May 2024
This page collects assemblies, annotations, and supplementary data for the Amphibolis antarctica and Posidonia australis genome assemblies.
The raw reads and assemblies are deposited in the SRA under BioProject PRJNA835502
Contents
Posidonia australis
Draft genome assembly:
P_australis_genome_bigger1kbp.fasta.gz
MAKER annotation:
GFF of all evidence: P_australis_genome_bigger1kbp.all.gff.gz
GFF of gene models only: P_australis_genome_bigger1kbp.all.gene_models.gff.gz
Proteins (fasta): P_australis_genome_bigger1kbp.all.maker.proteins.fasta.gz
Transcripts/CDS (fasta): P_australis_genome_bigger1kbp.all.maker.transcripts.fasta.gz
Amphibolis antarctica
Draft genome assembly:
A_antarctica_genome_bigger1kbp.fasta.gz
MAKER annotation:
GFF of all evidence: A_antarctica_genome_bigger1kbp.all.gff.gz
GFF of gene models only: A_antarctica_genome_bigger1kbp.all.gene_models.gff.gz
Proteins (fasta): A_antarctica_genome_bigger1kbp.all.maker.proteins.fasta.gz
Transcripts/CDS (fasta): A_antarctica_genome_bigger1kbp.all.maker.transcripts.fasta.gz
Chloroplast assemblies and annotations
Annotations (gff):
Annotations (genbank):
Assemblies
EDTA results
These are EDTA TE libraries, annotated using TEfinder using rexdb-plant. I renamed the TE names, if TEfinder had no hit, I used the EDTA name.
For example, this is the TEfinder output:
>TE_00000000#Unknown TE_00000000#DNA/DTC
Saying that TEfinder does not know the class, but EDTA has it under DNA/DTC based on the tool that predicted it.
I replaced these cases with a small script, this is the final name in the files below in cases where TEfinder could not find a class:
>TE_00000000#DNA/DTC TE_00000000#DNA/DTC
Amphibolis antarctica: A_antarctica_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz
Posidonia australis: P_australis_genome_bigger1kbp.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz
Zostera muelleri: Zmu_v1_scaffolds.big1k.merged_scaffolds.renamed.fa.mod.EDTA.TElib.fa.rexdb.cls.renamed.lib.fa.gz
Zostera marina: Zostera_marina.mainGenome.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz
