Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts

<strong><em>Pentalonia nigronervosa</em> v1 frozen release</strong> Genome assembly: Pentalonia_nigronervosa.v1.scaffolds.fa.gz BRAKER2 gene models: Pentalonia_nigronervosa.v1.scaffolds.gff BRAKER2 protein sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.cds.fa InterProScan functional annotation: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.interproscan.tsv <em>Pentalonia nigronervosa</em> v1 mitochondrial genome: Pentalonia_nigronervosa.v1.mt_genome.fa <em>Buchnera aphidicola</em> (BPn) scaffolds: Buchnera_aphidicola_BPn.scaffolds.fa <em>Wolbachia</em> (WolPenNig) scaffolds: Wolbachia_WolPenNig.scaffolds.fa <strong><em>Myzus cerasi </em>v1.2 frozen release</strong> Genome assembly: Myzus_cerasi.v1.2.scaffolds.fa BRAKER2 gene models: Myzus_cerasi.v1.2.scaffolds.gff BRAKER2 protein sequences: Myzus_cerasi.v1.2.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_cerasi.v1.2.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Myzus_cerasi.v1.2.scaffolds.gff.cds.fa <strong>Aphid orthogroups and species tree</strong> Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv Single copy conserved orthogroups used for species tree: Orthogroups_for_concatenated_alignment.txt Species tree alignment: SpeciesTreeAlignment.fa Rooted species tree: SpeciesTree_rooted.nwk <strong>Bash script to run k-mer based assembly deduplication pipeline</strong> File: disco_filter_dups.v1.1.sh This script will parse a discovar de novo assembly and remove scaffolds likely to be haplotigs based on their k-mer content and a self alignment of the assembly (see manuscript for details). The input discovar assembly needs to have white space in scaffold IDs replaced with "_" before running. Illumina reads should be unzipped before running. Usage: <pre><code class="language-bash">sh disco_filter_dups.sh &lt;./path_to_assembly&gt; &lt;./path_to_r1&gt; &lt;./path_to_r2&gt; &lt;homozyzgous_lower_cov&gt; &lt;homozyzgous_upper_cov&gt; &lt;nucmer_id_cutoff&gt; &lt;nucmer_cov_cutoff&gt; &lt;assembly_output_prefix&gt; &lt;threads&gt; &lt;./working_dir&gt;</code></pre>