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Probe sets

This directory contains some of the probe sets designed with CATCH:

  • V-All.250k.201810.fasta.gz: 249,999 probes that target genomes of all viruses known to infect humans, using sequence data through 2018-10 (588 species)
  • V-All.350k.201810.fasta.gz: 349,999 probes that target genomes of all viruses known to infect humans, using sequence data through 2018-10 (588 species)
  • V-All.700k.201810.fasta.gz: 699,999 probes that target genomes of all viruses known to infect humans, using sequence data through 2018-10 (588 species)
  • V-All.201606.fasta.gz: 349,998 probes that target genomes of all viruses known to infect humans, using sequence data through 2016-06 (356 species); V-All.201606.trimmed.fasta.gz is this same probe set with bases trimmed on the 3' end to meet synthesis cycle limits
  • V-WAfr.201506.fasta.gz: 44,995 probes that target genomes of viruses commonly circulating in West Africa, using sequence data through 2015-06 (23 species); this includes reverse complements as well, for 89,990 probes in total
  • V-Flu.45k.201810.fasta.gz: 44,848 probes that target genomes of influenza A, B, and C viruses, using sequence data through 2018-10; this includes reverse complements as well, for 89,696 probes in total
  • V-Flu.6k.201810.fasta.gz: 5,999 probes that target genomes of influenza A, B, and C viruses, using sequence data through 2018-10; this includes reverse complements as well, for 11,998 probes in total
  • V-Respiratory.100k.202001.fasta.gz: 99,814 probes that target genomes of respiratory-related viruses, including SARS-CoV-2, using sequence data through 2020-02-18 (namely: HRSV, HMPV, HPIVs, known human-infecting coronaviruses, Human mastadenovirus A-G, Enterovirus A-E, Rhinovirus A/B/C, influenza A/B/C). Note that this targets all sequence data from the SARS-related coronavirus species, including bat and pangolin SARS-like CoV sequences.
  • V-MM.201603.fasta.gz: 6,219 probes that target genomes of measles and mumps viruses, using sequence data through 2016-03; this includes reverse complements as well, for 12,438 probes in total
  • V-ZC.201602.fasta.gz: 6,171 probes that target genomes of chikungunya and Zika viruses, using sequence data through 2016-02; this includes reverse complements as well, for 12,342 probes in total

Note that there are 20 nt PCR adapters on both ends of probes in V-WAfr.201506.fasta.gz, V-Flu.45k.201810.fasta.gz, V-Flu.6k.201810.fasta.gz, V-MM.201603.fasta.gz, and V-ZC.201602.fasta.gz.