protein blastocystis sp subtype 4 xp 014529703  (ATCC)

Journal: mBio

Article Title: Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

doi: 10.1128/mbio.00699-25

Figure Lengend Snippet: Comparison of methods (Eukfinder_short, Refmapping, Eukfinder_long, EukRep, and Tiara) to recover Blastocystis ST1 genomes in eight datasets consisting of bacterial mock metagenomic data (mix-51) with varying amounts of randomly selected Blastocystis ST1 Illumina sequencing reads. (a) The plot of the total length of Blastocystis ST1 contigs recovered by each method. (b) Plot of weighted single copy genes (SCG) (number of SCGs detected corrected by gene completion). (c) The plot of recovered Blastocystis ST1 total length using reference data sets excluding ST1. Eukfinder_short was reassessed with databases excluding the ST1 genome, but including other Blastocystis genomes, (woST1), and with all Blastocystis genomes excluded (woBlasto). Refmapping was reassessed using genomes from ST2-9 as the reference .

Article Snippet: To test Eukfinder’s capabilities, we used simulated sequencing read files from a synthetic metagenome data set and randomly selected reads from the Illumina sequencing data set that generated the published genome of Blastocystis sp. ST1 (ATCC 50177/Nand II).

Techniques: Comparison, Illumina Sequencing

Journal: mBio

Article Title: Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

doi: 10.1128/mbio.00699-25

Figure Lengend Snippet: Precision and recall of the genomes recovered by Eukfinder_long, EukRep, and Tiara. (a) Average precision, measured as the fraction of true Blastocystis reads among all reads assigned as Blastocystis , and (b) average recall, measured as the fraction of Blastocystis reads that were recovered, at each read depth for the three long-read methods (Eukfinder_long, EukRep, and Tiara). Precision = true positives/(true positives + false positives). Recall = true positives/(true positives + false negatives). (c) The fraction of Blastocystis recovered from each mock community data set was assessed using QUAST using the true Blastocystis contigs (Individual Ref, based on input reads rather than complete reference genome) as the reference.

Article Snippet: To test Eukfinder’s capabilities, we used simulated sequencing read files from a synthetic metagenome data set and randomly selected reads from the Illumina sequencing data set that generated the published genome of Blastocystis sp. ST1 (ATCC 50177/Nand II).

Techniques:

Journal: mBio

Article Title: Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

doi: 10.1128/mbio.00699-25

Figure Lengend Snippet: Blastocystis ST3 and ST4 genomes recovered from eight human gut metagenome samples (3A–D and 4A–D, ) using Refmapping, Eukfinder_short, Eukfinder_long, EukRep, and Tiara. Genome completeness in ST3 containing samples (Refmapping reference genome ST3 ZGR) based on (a) total length (10 Mbp) and (b) number of SCGs detected using BUSCO (stramenophile_odb10). Genome completeness in ST4 containing samples (Refmapping reference genome ST4 WR1) based on (c) total length (10 Mbp) and (d) number of SCGs detected using BUSCO (stramenophile_odb10). Reanalysis of Refmapping ST4 genome completeness using reference genome ST4 BT1, (e) total length (10 Mbp), and (f) number of SCGs detected using BUSCO (stramenophile_odb10). Tiara was run with a kmer of 4 and a probability threshold of 0.7, and Refmapping was run in local mode. Lines representing reference genome sizes are shown for Blastocystis ST3 ZGR (dash), ST4 WR1 (dash-dot), and ST4 BT1 (dotted) for comparison.

Article Snippet: To test Eukfinder’s capabilities, we used simulated sequencing read files from a synthetic metagenome data set and randomly selected reads from the Illumina sequencing data set that generated the published genome of Blastocystis sp. ST1 (ATCC 50177/Nand II).

Techniques: Comparison

Journal: mBio

Article Title: Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

doi: 10.1128/mbio.00699-25

Figure Lengend Snippet: Comparison of the methods (Eukfinder_long, EukRep, Tiara, Eukfinder_short, and Refmapping) to recover Blastocystis mitochondrial related organellar (MRO) genomes from the eight human gut metagenome data sets, (a) Total length of MRO genomes (10 kbp); (b) number of contigs recovered. The MRO reference genome size for ST3 (dashed line) and ST4 (dashed-dotted line) is shown.

Article Snippet: To test Eukfinder’s capabilities, we used simulated sequencing read files from a synthetic metagenome data set and randomly selected reads from the Illumina sequencing data set that generated the published genome of Blastocystis sp. ST1 (ATCC 50177/Nand II).

Techniques: Comparison