Draft Whole-Genome Sequence of Xenorhabdus nematophila strain SC 0516... - SRA

SRX8685352: Draft Whole-Genome Sequence of Xenorhabdus nematophila strain SC 0516 associated with entomopathogenic nematodes host Steinernema carpocapsae
1 ILLUMINA (Illumina MiSeq) run: 3.9M spots, 595M bases, 297Mb downloads

Design: The reads quality was analyzed with FastQC. The Illumina adapter sequences were removed using the ILLUMINACLIP trimming step of Trimmomatic v0.39 program. Poor quality bases from Illumina paired-end reads were removed using the DynamicTrim algorithm of SolexaQA++ v3.1.7.1 software package with Phred quality score Q=13. The paired-end reads were de novo assembled using the SPAdes v3.14.1 program with the following options: i) only runs assembly module (--only-asembler); ii) reduce the number of mismatches (--careful); and iii) k-mer lengths between 21 to 71 that generated 248 contigs. Contigs with length less than 500 bp were discarded and the remaining ones used for a multi-draft-based analysis using the genome of Xenorhabdus nematophila strain YL001 through MeDuSa v1.6 scaffolder. A final assembly polishing step was performed by remapping the quality-filtered sequence reads on the ordered scaffolds using BWA and passing the resulting sorted binary alignments to SAMtools for indexing. The indexed alignments were used by Pilon v1.23.

Submitted by: Universidad Autonoma del Estado de Morelos

Study: Xenorhabdus nematophila strain SC 0516

PRJNA644662 • SRP270862 • All experiments • All runs

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Xenorhabdus nematophila is naturally a symbiont of the entomopathogenic nematode Steinernema carpocapsae. X. nematophila colonizes a specialized region of the anterior intestine of S. carpocapsae called the receptacle of the infective juvenile stage of the nematode and infects larvae of different insects.

Sample: Draft Whole-Genome Sequence of Xenorhabdus nematophila strain SC 0516 associated with entomopathogenic nematodes host Steinernema carpocapsae

SAMN15470407 • SRS6964264 • All experiments • All runs

Organism: Xenorhabdus nematophila

Library:

Name: SC0516

Instrument: Illumina MiSeq

Strategy: WGS

Source: GENOMIC

Selection: PCR

Layout: PAIRED

Runs: 1 run, 3.9M spots, 595M bases, 297Mb

Run	# of Spots	# of Bases	Size	Published
SRR12170536	3,914,704	595M	297Mb	2020-07-10

ID:: 11301404

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