Journal: bioRxiv

Article Title: TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection

doi: 10.1101/2025.07.16.664785

Figure Lengend Snippet: General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s Refseq database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.

Article Snippet: In TaxTriage with access to the external internet, the default pipeline uses the classification output to identify the species to be downloaded from the National Center for Biotechnology Information (NCBI) file transfer protocol (FTP) genomes repository of RefSeq representative assemblies.

Techniques: Generated, In Silico

Journal: BMC Bioinformatics

Article Title: EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality

doi: 10.1186/s12859-021-04480-2

Figure Lengend Snippet: EvalDNA quality scores for chromosomes from various genome assemblies. A EvalDNA quality scores for chromosomes from CH PICR, CH 2013 RefSeq, and the mouse, rat, human, cow, and rice reference genome assemblies. B EvalDNA quality scores for the same chromosomes but calculated using a model that does not include the normalized N50 metric

Article Snippet: The two Illumina-only assemblies included the 2013 CH RefSeq assembly [ ] and the 2013 chromosome sorted assembly (CSA) [ ].

Techniques: