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## TheiaMeta_Panel_Illumina_PE_PHB

TheiaMeta_Panel was created initially for the Illumina Viral Surveillance Panel; however, it can be used for any panel that is sequenced using Illumina paired-end reads if the appropriate taxon IDs are provided. TheiaMeta_Panel performs taxonomic binning, and then assembles the bins into contigs. If the contigs are associated with a supported organism, genomic characterization will be performed.
TheiaMeta_Panel_Illumina_PE was created initially for the [Illumina Viral Surveillance Panel](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/viral-surveillance-panel.html)[^1]; however, it can be used for any panel that is sequenced using Illumina paired-end reads if the appropriate taxon IDs are provided. TheiaMeta_Panel performs taxonomic binning, and then assembles the bins into contigs. If the contigs are associated with a supported organism, genomic characterization will be performed.

[^1]: We are not affiliated with Illumina, Inc. The mention of the Illumina Viral Surveillance Panel is for informational purposes only.

??? toggle "**What organisms and taxon IDs are identified by default?**"
The Illumina VSP panel contains over 224 viral species, of which 163 can be identified in the default Kraken2 viral database.

Accordingly, the following 163 taxon IDs are used by default in TheiaMeta_Panel_Illumina_PE. Feel free to search this table to see if your organism of interest is included.

<div class="searchable-table" markdown="1">

| **Taxon ID** | **Organism Name in Illumina VSP Panel** |
|---|---|
| 10804 | Adeno-associated virus 2 (AAV2) |
| 1313215 | Aichi virus 1 (AiV-A1) |
| 2849717  | Aigai virus (AIGV) |
| 1980456 | Andes virus (ANDV) |
| 1424613 | Anjozorobe virus (ANJV) |
| 90961 | Australian bat lyssavirus (ABLV) |
| 3052470 | Bayou virus (BAYV) |
| 3052490 | Black Creek Canal virus (BCCV) |
| 2010960 | Bombali virus (BOMV) |
| 1618189 | Bourbon virus (BRBV) |
| 565995 | Bundibugyo virus (BDBV) |
| 80935 | Cache Valley virus (CVV) |
| 35305 | California encephalitis virus (CEV) |
| 1221391 | Cedar virus (CedV) |
| 3052302 | Chapare virus (CHAPV) |
| 37124 | Chikungunya virus (CHIKV) |
| 169173 | Choclo virus (CHOV) |
| 46839 | Colorado tick fever virus (CTFV) |
| 138948 | Coxsackievirus A |
| 138949 | Coxsackievirus B |
| 3052518 | Crimean-Congo hemorrhagic fever virus (CCHFV) |
| 11053 | Dengue Virus 1 |
| 11060 | Dengue Virus 2 |
| 11069 | Dengue Virus 3 |
| 11070 | Dengue Virus 4 |
| 3052477 | Dobrava virus (DOBV) |
| 38767 | Duvenhage virus (DUVV) |
| 11021 | Eastern equine encephalitis virus (EEEV) |
| 138951 | Enterovirus D |
| 10376 | Epstein-Barr virus (EBV) |
| 57482 | European bat lyssavirus 1 |
| 57483 | European bat lyssavirus 2 |
| 2847089 | Ghana virus (GhV) |
| 3052307 | Guanarito virus (GTOV) |
| 3052480 | Hantaan virus (HTNV) |
| 1216928 | Heartland virus (HRTV) |
| 3052223 | Hendra virus (HeV) |
| 12092 | Hepatitis A virus (HAV) |
| 3052230 | Hepatitis C virus (HCV) |
| 12475 | Hepatitis D virus (HDV) |
| 10298 | Herpes simplex virus 1 (HSV1) |
| 129875 | Human adenovirus A |
| 108098 | Human adenovirus B |
| 129951 | Human adenovirus C |
| 130310 | Human adenovirus D |
| 130308 | Human adenovirus E |
| 130309 | Human adenovirus F |
| 536079 | Human adenovirus G |
| 11137 | Human coronavirus 229E (HCoV_229E) |
| 290028 | Human coronavirus HKU1 (HCoV_HKU1) |
| 277944 | Human coronavirus NL63 (HCoV_NL63) |
| 31631 | Human coronavirus OC43 (HCoV_OC43) |
| 10359 | Human cytomegalovirus (HCMV) |
| 11676 | Human immunodeficiency virus 1 (HIV-1) |
| 11709 | Human immunodeficiency virus 2 (HIV-2) |
| 162145 | Human metapneumovirus (HMPV) |
| 333760 | Human papillomavirus 16 (HPV16; high-risk) |
| 333761 | Human papillomavirus 18 (HPV18; high-risk) |
| 333762 | Human papillomavirus 26 (HPV26) |
| 12730 | Human parainfluenza virus 1 (HPIV-1) |
| 2560525 | Human parainfluenza virus 2 (HPIV-2) |
| 11216 | Human parainfluenza virus 3 (HPIV-3) |
| 2560526  | Human parainfluenza virus 4 (HPIV-4) |
| 1803956  | Human parechovirus (HPeV) |
| 10798  | Human parvovirus B19 (B19V) |
| 746830 | Human polyomavirus 6 (HPyV6) |
| 746831 | Human polyomavirus 7 (HPyV7) |
| 943908 | Human polyomavirus 9 (HPyV9) |
| 208893 | Human respiratory syncytial virus A (HRSV-A) |
| 114727 | Influenza A virus (H1N1) |
| 114729 | Influenza A virus (H2N2) |
| 119210 | Influenza A virus (H3N2) |
| 102793 | Influenza A virus (H5N1) |
| 333278 | Influenza A virus (H7N9) |
| 102796 | Influenza A virus (H9N2) |
| 11520 | Influenza B virus |
| 11552 | Influenza C virus |
| 35511 | Jamestown Canyon virus (JCV) |
| 11072 | Japanese encephalitis virus (JEV) |
| 10632 | JC polyomavirus (JCPyV) |
| 2169991 | Junin virus (JUNV) |
| 1891764 | KI polyomavirus (KIPyV) |
| 33743 | Kyasanur Forest disease virus (KFDV) |
| 11577 | La Crosse virus (LACV) |
| 38766 | Lagos bat virus (LBV) |
| 3052489 | Laguna Negra virus (LANV) |
| 3052310 | Lassa virus (LASV) |
| 1965344 | LI polyomavirus (LIPyV) |
| 3052148 | Lloviu virus (LLOV) |
| 3052314 | Lujo virus (LUJV) |
| 3052303 | Lymphocytic choriomeningitis virus (LCMV) |
| 3052317 | Machupo virus (MACV) |
| 1239565 | Mamastrovirus 1 (MAstV1) |
| 1239570 | Mamastrovirus 6 (MAstV6) |
| 1239573 | Mamastrovirus 9 (MAstV9) |
| 238817 | Maporal virus (MAPV) |
| 3052505 | Marburg virus (MARV) |
| 59301 | Mayaro virus (MAYV) |
| 11234 | Measles virus (MV) |
| 152219 | Menangle virus (MenV) |
| 493803 | Merkel cell polyomavirus (MCPyV) |
| 1335626 | Middle East respiratory syndrome-related coronavirus (MERS-CoV) |
| 1474807 | Mojiang virus (MojV) |
| 12538 | Mokola virus (MOKV) |
| 10244 | Monkeypox virus (MPV) |
| 2560602 | Mumps virus (MuV) |
| 11079 | Murray Valley encephalitis virus (MVEV) |
| 1203539 | MW polyomavirus (MWPyV) |
| 1497391 | New Jersey polyomavirus (NJPyV) |
| 3052225 | Nipah virus (NiV) |
| 142786 | Norovirus |
| 12542 | Omsk hemorrhagic fever virus (OHFV) |
| 2169701 | Onyong-nyong virus (ONNV) |
| 118655 | Oropouche virus (OROV) |
| 138950 | Poliovirus |
| 11083 | Powassan virus (POWV) |
| 11587 | Punta Toro virus (PTV) |
| 3052493 | Puumala virus (PUUV) |
| 11292 | Rabies virus (RABV) |
| 186539 | Reston virus (RESTV) |
| 147711 | Rhinovirus A (RV-A) |
| 147712 | Rhinovirus B (RV-B) |
| 463676 | Rhinovirus C (RV-C) |
| 11588 | Rift Valley fever virus (RVFV) |
| 11029 | Ross River virus (RRV) |
| 28875 | Rotavirus A (RVA) |
| 28876 | Rotavirus B (RVB) |
| 36427 | Rotavirus C (RVC) |
| 1348384 | Rotavirus H (RVH) |
| 11041 | Rubella virus (RuV) |
| 2907957 | Sabia virus (SBAV) |
| 1330524 | Salivirus A (SaV-A) |
| 3052496 | Sangassou virus (SANGV) |
| 95341 | Sapovirus |
| 11033 | Semliki Forest virus (SFV) |
| 3052498 | Seoul virus (SEOV) |
| 2901879 | Severe acute respiratory syndrome coronavirus (SARS-CoV) |
| 2697049 | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) |
| 1003835 | Severe fever with thrombocytopenia syndrome virus (SFTSV) |
| 1891767 | Simian virus 40 (SV40) |
| 3052499 | Sin nombre virus (SNV) |
| 11034 | Sindbis virus (SINV) |
| 11580 | Snowshoe hare virus (SSHV) |
| 1452514 | Sosuga virus (SoRV) |
| 11080 | St. Louis encephalitis virus (SLEV) |
| 1277649 | STL polyomavirus (STLPyV) |
| 186540 | Sudan virus (SUDV) |
| 1608084 | Tacheng tick virus 2 (TcTV-2) |
| 45270 | Tahyna virus (TAHV) |
| 186541 | Tai Forest virus (TAFV) |
| 11084 | Tick-borne encephalitis virus (TBEV) |
| 68887 | Torque teno virus (TTV) |
| 862909 | Trichodysplasia spinulosa-associated polyomavirus (TSPyV) |
| 3052503 | Tula virus (TULV) |
| 64286 | Usutu virus (USUV) |
| 10255 | Variola virus (VARV) |
| 11036 | Venezuelan equine encephalitis virus (VEEV) |
| 11082 | West Nile virus (WNV) |
| 11039 | Western equine encephalitis virus (WEEV) |
| 440266 | WU polyomavirus (WUPyV) |
| 11089 | Yellow fever virus (YFV) |
| 186538 | Zaire ebolavirus(EBOV) |
| 64320 | Zika virus (ZIKV) |

</div>

!!! tip "Make your own list of taxon IDs"
You may want to make your own list of taxon IDs if you know your sample is likely to contain a specific organism or group of organisms. You can find taxon IDs in the [NCBI Taxonomy Browser](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi).

In Terra, you provide your created list of taxon IDs as an array of integers for the `taxon_ids` optional input variable, like this: `[1, 2, 3, 4, 5]`. Just replace the numbers in this example with the taxon IDs you want to use.

### Inputs

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| Software Documentation | <https://github.com/DerrickWood/kraken2/wiki> |
| Original Publication(s) | [Improved metagenomic analysis with Kraken 2](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0) |

??? task "`KrakenTools extract_kraken_reads`: Read Binning"
??? task "`extract_kraken_reads` from KrakenTools: Read Binning"
KrakenTools is a collection of scripts that can be used to help downstream analysis of Kraken2 results. In particular, this task uses the `extract_kraken_reads` script, which extracts reads classified at any user-specified taxonomy IDs. All parent and children reads of the specified taxonomic ID are also extracted.

!!! techdetails "KrakenTools Technical Details"
Expand Down Expand Up @@ -199,21 +381,9 @@ TheiaMeta_Panel was created initially for the Illumina Viral Surveillance Panel;

</div>

## References (if applicable)

>**Trimmomatic:** Anthony M. Bolger and others, Trimmomatic: a flexible trimmer for Illumina sequence data, *Bioinformatics*, Volume 30, Issue 15, August 2014, Pages 2114–2120, <https://doi.org/10.1093/bioinformatics/btu170>
<!-- -->
>**Fastq-Scan:** <https://github.com/rpetit3/fastq-scan>
<!-- -->
>**metaSPAdes:** Sergey Nurk and others, metaSPAdes: a new versatile metagenomic assembler, *Genome Res.* 2017 May; 27(5): 824–834., <https://doi.org/10.1101%2Fgr.213959.116>
<!-- -->
>**Pilon:** Bruce J. Walker and others. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. *Plos One.* November 19, 2014. <https://doi.org/10.1371/journal.pone.0112963>
<!-- -->
>**Minimap2:** Heng Li, Minimap2: pairwise alignment for nucleotide sequences, *Bioinformatics*, Volume 34, Issue 18, September 2018, Pages 3094–3100, <https://doi.org/10.1093/bioinformatics/bty191>
<!-- -->
>**QUAST:** Alexey Gurevich and others, QUAST: quality assessment tool for genome assemblies, *Bioinformatics*, Volume 29, Issue 8, April 2013, Pages 1072–1075, <https://doi.org/10.1093/bioinformatics/btt086>
<!-- -->
>**Samtools:** Li, Heng, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16): 2078-2079.
<!-- -->
>**Bcftools:** Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li. Twelve years of SAMtools and BCFtools. GigaScience, Volume 10, Issue 2, February 2021, giab008, <https://doi.org/10.1093/gigascience/giab008>
<!-- -->
#### The `results_by_taxon_tsv` Output File

This file contains the

## References

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File read1
File read2
# default taxon IDs for Illumina VSP panel
Array[Int] taxon_ids
# = [10244, 10255, 10298, 10359, 10376, 10632, 10804, 11021, 11029, 11033, 11034, 11036, 11039, 11041, 11053, 11060, 11069, 11070, 11072, 11079, 11080, 11082, 11083, 11084, 11089, 11137, 11234, 11292, 11520, 11552, 11577, 11580, 11587, 11588, 11676, 11709, 12092, 12475, 12538, 12542, 28875, 28876, 31631, 33743, 35305, 35511, 36427, 37124, 38766, 38767, 45270, 46839, 57482, 57483, 59301, 64286, 64320, 68887, 80935, 90961, 95341, 102793, 102796, 108098, 114727, 114729, 118655, 119210, 129875, 129951, 130308, 130309, 130310, 138948, 138949, 138950, 138951, 147711, 147712, 152219, 162145, 169173, 186538, 186539, 186540, 186541, 238817, 277944, 290028, 333278, 333760, 333761, 333762, 440266, 463676, 493803, 536079, 565995, 862909, 1003835, 1216928, 1221391, 1239565, 1239570, 1239573, 1277649, 1313215, 1330524, 1335626, 1348384, 1424613, 1452514, 1474807, 1497391, 1608084, 1618189, 1891764, 1891767, 1965344, 1980456, 2010960, 2169701, 2169991, 2560525, 2560602, 2697049, 2847089, 2901879, 2907957, 3052148, 3052223, 3052225, 3052230, 3052302, 3052307, 3052310, 3052314, 3052470, 3052477, 3052480, 3052489, 3052490, 3052493, 3052496, 3052499, 3052503, 3052505, 3052518, 10798, 11216, 1203539, 12730, 142786, 1803956, 208893, 2560526, 2849717, 3052303, 3052317, 3052498, 746830, 746831, 943908]
Array[Int] taxon_ids = [10244, 10255, 10298, 10359, 10376, 10632, 10804, 11021, 11029, 11033, 11034, 11036, 11039, 11041, 11053, 11060, 11069, 11070, 11072, 11079, 11080, 11082, 11083, 11084, 11089, 11137, 11234, 11292, 11520, 11552, 11577, 11580, 11587, 11588, 11676, 11709, 12092, 12475, 12538, 12542, 28875, 28876, 31631, 33743, 35305, 35511, 36427, 37124, 38766, 38767, 45270, 46839, 57482, 57483, 59301, 64286, 64320, 68887, 80935, 90961, 95341, 102793, 102796, 108098, 114727, 114729, 118655, 119210, 129875, 129951, 130308, 130309, 130310, 138948, 138949, 138950, 138951, 147711, 147712, 152219, 162145, 169173, 186538, 186539, 186540, 186541, 238817, 277944, 290028, 333278, 333760, 333761, 333762, 440266, 463676, 493803, 536079, 565995, 862909, 1003835, 1216928, 1221391, 1239565, 1239570, 1239573, 1277649, 1313215, 1330524, 1335626, 1348384, 1424613, 1452514, 1474807, 1497391, 1608084, 1618189, 1891764, 1891767, 1965344, 1980456, 2010960, 2169701, 2169991, 2560525, 2560602, 2697049, 2847089, 2901879, 2907957, 3052148, 3052223, 3052225, 3052230, 3052302, 3052307, 3052310, 3052314, 3052470, 3052477, 3052480, 3052489, 3052490, 3052493, 3052496, 3052499, 3052503, 3052505, 3052518, 10798, 11216, 1203539, 12730, 142786, 1803956, 208893, 2560526, 2849717, 3052303, 3052317, 3052484, 3052498, 746830, 746831, 943908]
# suggest using a workspace element if user wants to modify?
Int minimum_read_number = 1000
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