The genome sequence of an ichneumonid wasp, Amblyjoppa fuscipennis (Wesmael, 1844)

We present a genome assembly from an individual male Amblyjoppa fuscipennis (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 278.5 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 35.62 kilobases in length.

[1]  K. Pruitt,et al.  GenBank 2024 Update. , 2023, Nucleic acids research.

[2]  Richard J. Challis,et al.  Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life , 2023, Wellcome open research.

[3]  Shane A. McCarthy,et al.  MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads , 2023, bioRxiv.

[4]  Cathy H. Wu,et al.  UniProt: the Universal Protein Knowledgebase in 2023 , 2022, Nucleic Acids Res..

[5]  Colin M. Diesh,et al.  JBrowse 2: a modular genome browser with views of synteny and structural variation , 2022, bioRxiv.

[6]  Shane A. McCarthy,et al.  YaHS: yet another Hi-C scaffolding tool , 2022, bioRxiv.

[7]  Seán G. Brady,et al.  Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications , 2021 .

[8]  Felipe A. Simão,et al.  BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes , 2021, Molecular biology and evolution.

[9]  H. Drost,et al.  Sensitive protein alignments at tree-of-life scale using DIAMOND , 2021, Nature Methods.

[10]  Heng Li,et al.  Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm , 2021, Nature Methods.

[11]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[12]  Sergey Koren,et al.  Towards complete and error-free genome assemblies of all vertebrate species , 2020, Nature.

[13]  Sven Nahnsen,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[14]  Mark Blaxter,et al.  BlobToolKit – Interactive Quality Assessment of Genome Assemblies , 2019, G3: Genes, Genomes, Genetics.

[15]  F. Delsuc,et al.  MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics , 2019, bioRxiv.

[16]  Srinivas Aluru,et al.  Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems , 2019, 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).

[17]  Nezar Abdennur,et al.  Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.

[18]  Brent S. Pedersen,et al.  Bioconda: sustainable and comprehensive software distribution for the life sciences , 2018, Nature Methods.

[19]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[20]  Vanessa Sochat,et al.  Singularity: Scientific containers for mobility of compute , 2017, PloS one.

[21]  Paolo Di Tommaso,et al.  Nextflow enables reproducible computational workflows , 2017, Nature Biotechnology.

[22]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[23]  Harald Barsnes,et al.  BioContainers: an open-source and community-driven framework for software standardization , 2017, Bioinform..

[24]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[25]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[26]  Dirk Merkel,et al.  Docker: lightweight Linux containers for consistent development and deployment , 2014 .

[27]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[28]  R. Nash,et al.  A catalogue of the Irish Ichneumonidae (Hymenoptera: Ichneumonoidea). , 2007 .

[29]  D. Wahl,et al.  The cladistics and biology of the Callajoppa genus-group (Hymenoptera: Ichneumonidae, Ichneumoninae) , 2002 .

[30]  M. Riedel,et al.  Ichneumonidae (Hymenoptera) new for the fauna of Norway, Part 3 , 2000 .

[31]  S. Chiu,et al.  A check list of ichneumonidae (hymenoptera) of Taiwan , 1984 .

[32]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .