Research graph
References from The chromosomal genome sequence of Pione sp. (Clionaida: Clionaidae) and its associated microbial metagenome sequences. Local targets link to admitted publications; unresolved targets remain external evidence.
Basic Local Alignment Search Tool.
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
UniProt: The Universal Protein Knowledgebase in 2023.
10.1093/nar/gkac1052 · 2023 · External reference
In situ measurements of photosynthetic irradiance responses of two Red Sea sponges growing under dim light conditions.
10.1007/s002270050353 · 1998 · External reference
High-quality metagenome assembly from long accurate reads with metaMDBG.
10.1038/s41587-023-01983-6 · 2024 · External reference
Pyrosequencing reveals sponge specific bacterial communities in marine sponges of the Red Sea, Saudi Arabia.
10.1016/j.sjbs.2019.05.002 · 2020 · External reference
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
10.1038/nbt.3893 · 2017 · External reference
10.1007/978-3-662-45201-1_27
10.1007/978-3-662-45201-1_27 · 2015 · External reference
Sensitive protein alignments at tree-of-life scale using DIAMOND.
10.1038/s41592-021-01101-x · 2021 · External reference
BlobToolKit – interactive quality assessment of genome assemblies.
10.1534/g3.119.400908 · 2020 · External reference
GTDB-Tk v2: Memory friendly classification with the genome taxonomy database.
10.1093/bioinformatics/btac672 · 2022 · External reference
Haplotype-resolved de novo assembly using phased assembly graphs with Hifiasm.
10.1038/s41592-020-01056-5 · 2021 · External reference
Twelve years of SAMtools and BCFtools.
10.1093/gigascience/giab008 · 2021 · External reference
MultiQC: Summarize analysis results for multiple tools and samples in a single report.
10.1093/bioinformatics/btw354 · 2016 · External reference
The nf-core framework for community-curated bioinformatics pipelines.
10.1038/s41587-020-0439-x · 2020 · External reference
Two Pione species (Hadromerida, Clionaidae) from the Red Sea: A taxonomical challenge.
10.1007/s13127-010-0027-x · 2010 · External reference
Gfastats: Conversion, evaluation and manipulation of genome sequences using assembly graphs.
10.1093/bioinformatics/btac460 · 2022 · External reference
Identifying and removing haplotypic duplication in primary genome assemblies.
10.1093/bioinformatics/btaa025 · 2020 · External reference
On the excavating powers of certain sponges belonging to the genus Cliona; with descriptions of several new species, and an allied generic form.
10.1080/03745485909494773 · 1849 · External reference
On the path to reference genomes for all biodiversity: Laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life.
10.1093/gigascience/giaf119 · 2025 · External reference
Significantly improving the quality of genome assemblies through curation.
10.1093/gigascience/giaa153 · 2021 · External reference
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
10.1093/molbev/msw046 · 2016 · External reference
Die Spongienfauna des Rothen Meeres (II. Hälfte) [the sponge fauna of the Red Sea (II. half)].
1891 · External reference
HiGlass: Web-based visual exploration and analysis of genome interaction maps.
10.1186/s13059-018-1486-1 · 2018 · External reference
On the phylogenetic relationships of hadromerid and poecilosclerid sponges.
10.1017/s0025315407058237 · 2007 · External reference
Singularity: Scientific containers for mobility of compute.
10.1371/journal.pone.0177459 · 2017 · External reference
Résultats scientifiques des campagnes de la “Calypso” III. V. Campagne 1951–1952 en Mer Rouge (suite). 11. Spongiaires de Mer Rouge recueillis par la “Calypso” (1951–1952) [scientific results of the “Calypso” campaigns III. V. Campaign 1951–1952 to the Red Sea (continued). 11. Red Sea sponges collected by the “Calypso” (1951–1952)].
1958 · External reference
Minimap2: Pairwise alignment for nucleotide sequences.
10.1093/bioinformatics/bty191 · 2018 · External reference
BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.
10.1093/molbev/msab199 · 2021 · External reference
Quantitative ecological analysis of a reef lagoon area near Aqaba (Gulf of Aqaba, Red Sea).
10.1007/bf02277991 · 1979 · External reference
Docker: Lightweight Linux containers for consistent development and deployment.
10.5555/2600239.2600241 · 2014 · External reference
Purification of a new dimeric protein from Cliona vastifica sponge, which specifically blocks a non-L-type calcium channel in mouse duodenal myocytes.
10.1124/mol.51.6.1042 · 1997 · External reference
dRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.
10.1038/ismej.2017.126 · 2017 · External reference
CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
10.1101/gr.186072.114 · 2015 · External reference
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.
10.1038/s41467-020-14998-3 · 2020 · External reference
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
10.1016/j.cell.2014.11.021 · 2014 · External reference
Towards complete and error-free genome assemblies of all vertebrate species.
10.1038/s41586-021-03451-0 · 2021 · External reference
Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies.
10.1186/s13059-020-02134-9 · 2020 · External reference
MAGScoT: A fast, lightweight and accurate bin-refinement tool.
10.1093/bioinformatics/btac694 · 2022 · External reference
The role of burrowing sponges in bioerosion.
10.1007/bf00345306 · 1975 · External reference
10.1007/978-1-4615-0747-5_19
10.1007/978-1-4615-0747-5_19 · 2002 · External reference
NCBI taxonomy: A comprehensive update on curation, resources and tools.
10.1093/database/baaa062 · 2020 · External reference
10.1007/978-3-540-77598-0_9
10.1007/978-3-540-77598-0_9 · 2008 · External reference
Prokka: Rapid prokaryotic genome annotation.
10.1093/bioinformatics/btu153 · 2014 · External reference
Photoadaptation of zooxanthellae in the sponge Cliona vastifica from the Red Sea, as measured in situ.
10.1007/s002270000482 · 2001 · External reference
MitoHiFi: A Python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.
10.1186/s12859-023-05385-y · 2023 · External reference
10.1109/ipdps.2019.00041
10.1109/ipdps.2019.00041 · 2019 · External reference
Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae).
10.1016/j.ympev.2010.03.030 · 2010 · External reference
InEx – a direct in situ method to measure filtration rates, nutrition, and metabolism of active suspension feeders.
10.4319/lom.2005.3.46 · 2005 · External reference
YaHS: Yet another Hi-C scaffolding tool.
10.1093/bioinformatics/btac808 · 2023 · External reference
Chemical versus mechanical bioerosion of coral reefs by boring sponges–lessons from Pione cf. vastifica.
10.1242/jeb.02627 · 2007 · External reference
