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. 2024 Jul 30;27(9):110614. doi: 10.1016/j.isci.2024.110614
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Brugia malayi adults NIH/NIAID Filariasis Research Reagent Resource Center via BEI Resources (Michalski et al.28) FR3 strain
Trichuris trichiura adults Peter Nejsum, Department of Clinical Medicine, Aarhus University N/A
Ancylostoma caninum third-stage larvae John M. Hawdon, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Baltimore strain
Chemicals, peptides, and recombinant proteins
DNA/RNA Shield Zymo Research, Irvine, CA, USA Cat#R1200-25
Critical commercial assays
Quick-DNA HMW MagBead Kit Zymo Research, Irvine, CA, USA Cat#D6060
Monarch® Pestle Set single-use microtube pestle New England Biolabs® Inc., Ipswich, MA, USA Cat#T3000L
Qubit™ 4 1X dsDNA High Sensitivity (HS) Assay ThermoFisher Scientific, Waltham, MA, USA Cat#Q33231
Agilent 2200 TapeStation System Genomic DNA ScreenTape and Reagents Agilent, Santa Clara, CA, USA Cat#5067-5365; 5067-5366
AMPure XP Beckman Coulter, Brea, CA, USA Cat#A63880
DNA Clean & Concentrator Magbee Kit Zymo Research, Irvine, CA, USA Cat#D4012
Ligation Sequencing Kit Oxford Nanopore Technologies, Oxford, United Kingdom Cat#SQK-LSK114
NEBNext® Companion Module for Oxford Nanopore Technologies® Ligation Sequencing New England Biolabs® Inc., Ipswich, MA, USA Cat#E7180S
xGen™ cfDNA & FFPE DNA Library Prep Kit Integrated DNA Technologies, Newark, NJ, USA Cat#10010207
Deposited data
Quality-controlled MinION and Illumina read data for Brugia malayi National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) BioProject accession ID PRJNA1074771; BioSample accession no. SAMN39888962
Quality-controlled MinION and Illumina read data for Trichuris trichiura National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) BioProject accession ID PRJNA1074771; BioSample accession no. SAMN39888963
Quality-controlled MinION and Illumina read data for Ancylostoma caninum National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) BioProject accession ID PRJNA1074771; BioSample accession no. SAMN39888964
Final assemblies generated for Brugia malayi National Center for Biotechnology Information (NCBI) Genome database Accession nos. GCA_037903335.1; GCA_037903345.1; GCA_037903365.1
Final assemblies generated for Trichuris trichiura National Center for Biotechnology Information (NCBI) Genome database Accession nos. GCA_037903355.1; GCA_037903375.1;GCA_037903465.1
Final assemblies generated for Ancylostoma caninum National Center for Biotechnology Information (NCBI) Genome database Accession nos. GCA_037903475.1; GCA_037903715.1; GCA_037903745.1
Reference genome for Brugia malayi Tracy et al.29 BioProject accession ID PRJNA10729
Reference genome for Trichuris trichiura Foth et al.38 BioProject accession ID PRJEB535
Reference genome for Trichuris trichiura Doyle et al.23 https://github.com/stephenrdoyle/ancient_trichuris/tree/master/02_data
Reference genome for Ancylostoma caninum International Helminth Genomes Consortium7 BioProject accession ID PRJNA72585
Mitochondrial reference genome for Ancylostoma caninum Xie et al.39 GenBank accession ID MN215971
Reference genomes for nematodes that parasitize animals WormBase ParaSite16,17 https://parasite.wormbase.org/species.html#Nematoda
Software and algorithms
MinKNOW v. 22.10.7; 22.10.10; 22.12.7 Oxford Nanopore Technologies https://community.nanoporetech.com/docs/prepare/library_prep_protocols/experiment-companion-minknow/v/mke_1013_v1_revdc_11apr2016/installing-minknow-on-linu
Guppy v. 6.3.4 Oxford Nanopore Technologies https://community.nanoporetech.com/downloads?from=support
NanoPlot v. 1.40.2 De Coster40 https://github.com/wdecoster/NanoPlot
Mash v. 2.2.2 Ondov et al.41 https://mash.readthedocs.io/en/latest/#
Minimap2 v. 2.16 Li42 https://github.com/lh3/minimap2
SAMtools v. 1.9 Danecek et al.43 https://github.com/samtools/samtools
fastp v. 0.23.2 Chen et al.44 https://github.com/OpenGene/fastp
BWA v. 0.7.17 Li and Durbin45 https://github.com/lh3/bwa
Jellyfish v. 2.3.0 Marçais and Kingsford46 https://github.com/gmarcais/Jellyfish
GenomeScope web-based graphical user interface Ranallo-Benavidez et al.44 https://github.com/schatzlab/genomescope
Canu v. 2.1 Koren et al.36 https://github.com/marbl/canu
wtdbg2 v. 0.0 Ruan and Li47 https://github.com/ruanjue/wtdbg2
Shasta 0.11.1 Shafin et al.48 https://github.com/chanzuckerberg/shasta
Flye v. 2.9.1-b1780 Kolmogorov et al.49 https://github.com/mikolmogorov/Flye
SeqKit v 0.10.1 Shen et al.50 https://bioinf.shenwei.me/seqkit/
BBMap v.38.84 Bushnell51 https://github.com/BioInfoTools/BBMap
purge_dups v. 1.2.5 Guan et al.52 https://github.com/dfguan/purge_dups
Racon v. 1.5.0 Vaser et al.53 https://github.com/isovic/racon
Medaka v. 1.7.2 Oxford Nanopore Technologies https://github.com/nanoporetech/medaka
Pilon v. 1.24 Walker et al.54 https://github.com/broadinstitute/pilon
MaSuRCA v. 4.1.0 Zimin et al.37 https://github.com/alekseyzimin/masurca
WENGAN v. 0.2 Di Genova et al.55 https://github.com/adigenova/wengan
HASLR v. 0.8a1 Haghshenas et al.56 https://github.com/vpc-ccg/haslr
K-mer Analysis Toolkit (KAT) v. 2.4.0 Mapleson et al.57 https://github.com/TGAC/KAT
BlobTools v. 1.1.1 Challis et al.58 https://github.com/DRL/blobtools
BLAST v. 2.14.0 Altschul et al.59 https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata
ggplot2 R package Wickham60 https://ggplot2-book.org/
R v. 4.3.0; 4.2.3 Core R Team61 https://cran.rstudio.com/
RStudio v. 2023.03.1; 2023.06.1 N/A https://posit.co/download/rstudio-desktop/
Geneious Prime v. 2022.0.1 Kearse et al.62 https://www.geneious.com/updates
QUAST v. 5.0.2 Gurevich et al.63 https://github.com/ablab/quast
compleasm v. 0.2.6 Huang and Li64 https://github.com/huangnengCSU/compleasm
GeMoMA v. 1.9 Keilwagen et al.65,66 https://www.jstacs.de/index.php/GeMoMa
AGAT v. 0.9.1 Dainat et al.67 https://github.com/NBISweden/AGAT
Biostrings R package v. 2.66.0 Pagès et al.68 https://bioconductor.org/packages/release/bioc/html/Biostrings.html