added relevant COI mock community info and rep seqs #92
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| # mock-coi1 | ||
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| DNA extracted from voucher arthropod specimen was amplified using ANML primers described in [Jusino et al. 2019](https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12951). PCR products were cloned into plasmid vectors and Sanger sequenced. While that paper describes a single mock community, the researchers in fact created a series of distinct mock samples with varying community membership. This mock community consists of a subset of the species described in their paper: specifically there are 24 representative COI sequences derived from 23 taxa. One of the distinct taxa (_Harmonia axyridis_) generated two distinct COI amplicons. The mock community used in this project consists of equimolar concentrations of plasmids, not post-plasmid PCR product. Taxonomic identities were assigned by a trained entomologist’s visual identification and were confirmed by manually aligning sequences to NCBI’s nt database. | ||
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| # Known Issues / Notes | ||
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| Note: | ||
| The mock sample described above was sequenced in conjunction with hundreds of bat guano samples in a single MiSeq run. All data are availble as BioSamples [here at NCBI](https://www.ncbi.nlm.nih.gov/bioproject/518082). Individual sequence data specific to the mock sample are found in the `dataset-metadata.tsv` document. | ||
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| These reads contain dual-index barcodes modeled after the Schloss lab [workflow described here](https://github.com/SchlossLab/MiSeq_WetLab_SOP/blob/master/MiSeq_WetLab_SOP.md). Reads were processed in QIIME2 as described in [this GitHub repo](https://github.com/devonorourke/tidybug/blob/master/docs/sequence_filtering.md#raw-sequence-data-processing). | ||
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There was a problem hiding this comment. it may be useful to provide a snippet of code showing how to import these reads into QIIME 2 (note that dual-index barcode support is now available in QIIME 2!) |
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| Taxonomic information is listed in the fasta header for each expected mock sequence. | ||
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| name value | ||
| citation NA | ||
| qiita-id NA | ||
| raw-data-url-forward-read https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8536507 | ||
| raw-data-url-reverse-read https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8536507 | ||
| raw-data-url-index-read NA | ||
| target-gene COI | ||
| target-subfragment NA | ||
| study-type marker-gene | ||
| sequencing-instrument illumina-miseq | ||
| physical-specimen-available No | ||
| contact-email devon@outermostlab.com | ||
| GitHub-repo https://github.com/devonorourke/tidybug |
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| SampleID BarcodeSequence LinkerPrimerSequence forwardPrimer-name forwardPrimer-seq reversePrimer-name reversePrimer-seq Description | ||
| mock.IM4p4L1 NA NA SD506 AATGATACGGCGACCACCGAGATCTACACATCGTACGTATGGTAATTCGGGTCAACAAATCATAAAGATATTGG SD711 CAAGCAGAAGACGGCATACGAGATAACTCTCGAGTCAGTCAGCCGGWACTAATCAATTTCCAAATCC alias-is-LibA-in-publication |
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| >MockIM3; KP954638;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Diptera,f:Culicidae,g:Aedes,s:Aedes vexans | ||
| GTCAACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAGTTTGATCAGGAATAGTAGGAACATCTTTAAGTATATTAATTCGTGCTGAATTAAGTCACCCAGGGATATTTATTGGAAATGATCAAATTTATAACGTAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCAATTATAATTGGAGGATTTGGAAATTGATTAGTTCC | ||
| >MockIM4; NC_022185;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Noctuidae,g:Agrotis,s:Agrotis ipsilon | ||
| GTCAACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGTATTTGAGCTGGAATAGTAGGAACTTCTTTAAGATTATTAATTCGAGCTGAACTAGGAAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACAATTGTTACAGCACATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTACC | ||
| >MockIM5; tax=k:Animalia,p:Arthropoda,c:Insecta,o:Hemiptera,f:Aphididae,g:Aphis,s:Aphis helianthi | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATATTTTTTATTTGGTATTTGATCAGGTATAATTGGATCTTCACTTAGAATTTTAATTCGATTAGAATTAAGTCAAATTAATTCAATTATTAATAATAACCAACTATATAATGTAATTGTTACAATTCATGCTTTTATTATAATTTTCTTTATAACTATACCAATTGTAATTGGTGGATTTGGAAATTGATTAATTCC | ||
| >MockIM7; tax=k:Animalia,p:Arthropoda,c:Insecta,o:Trichoptera,f:Leptoceridae,g:Ceraclea,s:Ceraclea maculata | ||
| GTCAACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGTGTATGATCTGGTCTTTTAGGCACATCCTTGAGAGTCTTAATTCGAACAGAGTTAGGGATAGTTGGATCATTAATTAAAAATGATCAAATTTATAACGTTTTAGTAACAGCTCATGCTTTTATTATAATTTTCTTTATAGTCATACCTATTATAATTGGAGGGTTTGGAAATTGATTAGTTCC | ||
| >MockIM10; GU092272;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Tortricidae,g:Choristoneura,s:Choristoneura rosaceana | ||
| GTCAACAAATCATAAAGATATTGGTACATTATATTTTATATTTGGAATTTGAGCAGGTATAGTAGGAACATCATTAAGATTATTAATTCGAGCTGAACTAGGAAATCCTGGATCTTTAATTGGTGATGATCAAATTTATAATACTATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTTCC | ||
| >MockIM15; GU689890;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Diptera,f:Bombyliidae,g:Lepidophora,s:Lepidophora lutea | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTTGGAGCCTGAGCAGGTATAGTAGGTACATCTTTAAGAATTCTTGTACGTGCCGAATTAGGACACCCTGGAGCATTAATTGGAGATGATCAAATCTATAATGTAATTGTTACAGCTCACGCTTTTATTATAATTTTCTTTATAGTAATACCTATTATAATTGGGGGATTTGGAAACTGATTGGTTCC | ||
| >MockIM16; GU093216;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Crambidae,g:Elophila,s:Elophila obliteralis | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATATTTCATTTTTGGTATTTGGGCAGGAATAGTAGGAACTTCTTTAAGATTATTAATTCGAGCTGAATTAGGAAATCCGGGATATTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATCATAATTTTTTTTATAGTTATACCTATTATAATTGGGGGATTTGGTAATTGATTAGTGCC | ||
| >MockIM20; EU443364;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Geometridae,g:Haematopis,s:Haematopis grataria | ||
| GTCAACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGAATCTGAGCCGGAATAATTGGAACCTCTTTAAGATTAATAATTCGAGCTGAATTAGGAGCTCCAGGACATTTAATTGGAGACGATCAAATTTATAATACTATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATGCCAATTATAATTGGAGGATTTGGAAATTGATTAGTGCC | ||
| >MockIM21; KR485316;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Coleoptera,f:Coccinellidae,g:Harmonia,s:Harmonia axyridis | ||
| GTCAACAAATCATAAAGATATTGGAACATTATACTTTTTATTTGGAATATGGGCAGGAATAGTAGGAACATCGTTAAGTATTTTAATTCGGTTAGAATTAGGAACTAGAGGAAGATTAATTGGAAGCGACCAAATTTATAATATAATTGTTACAGCTCATGCTTTCATTATAATTTTCTTTATAGTAATACCTATTATAATTGGGGGTTTTGGAAATTGATTAGTTCC | ||
| >MockIM23; KR483852;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Coleoptera,f:Coccinellidae,g:Harmonia,s:Harmonia axyridis | ||
| GTCAACAAATCATAAAGATATTGGAACATTATACTTTTTATTTGGAATATGAGCAGGAATAGTAGGAACATCGCTAAGTATTTTAATTCGGTTAGAATTAGGGACTAGAGGAAGATTAATTGGAAACGACCAAATTTATAATATAATTGTTACAGCTCATGCTTTCATTATAATTTTCTTTATAGTAATACCTATTATAATTGGAGGTTTTGGAAATTGATTAGTTCC | ||
| >MockIM27; HQ978960;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Coleoptera | ||
| GTCAACAAATCATAAAGATATTGGAACTTTGTATTTTATTTTCGGTGCTTGAGCAGGTATAGTAAGAACATCTTTAAGAATCCTTATTCGAGCTGAATTAGGTAATCCCGGAACATTAATTGGTGATGACCAAATTTATAACGTAATTGTAACTGCACATGCTTTTATCATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGGTTTGGAAATTGATTAGTTCC | ||
| >MockIM28; AB747649;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Erebidae,g:Hyphantria,s:Hyphantria cunea | ||
| GTCAACAAATCATAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACATCTTTAAGATTGTTAATTCGAGCAGAATTAGGAAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACAGCTCATGCTTTTATTATAATTTTTTTCATAGTTATACCAATTATAATTGGAGGATTTGGAAATTGATTAGTCCC | ||
| >MockIM29; KJ380118;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Erebidae,g:Hypena,s:Hypena scabra | ||
| GTCAACAAATCATAAAGATATTGGTACTTTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACTTCTTTAAGATTATTAATTCGTGCAGAATTAGGAACTCCCGGATCATTAATTGGTGATGATCAAATTTATAATACTATTGTCACAGCTCACGCTTTCATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCC | ||
| >MockIM32; JQ662689;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Ephemeroptera | ||
| GTCAACAAATCATAAAGATATTGGTACCCTTTATTTTATTTTTGGAGCTTGGGCAGGAATAGTAGGAACTTCTTTGAGCTTATTAATCCGAGCTGAACTTGGTCAGCCTGGTTCACTTATTGGGGATGACCAAATTTATAATGTTATTGTAACAGCCCACGCCTTCATTATAATTTTCTTTATAGTGATACCAATTATAATTGGAGGATTTGGTAATTGATTAGTACC | ||
| >MockIM33; HM374985;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Neuroptera | ||
| GTCAACAAATCATAAAGATATTGGAGTTTTATATTTTATTTTTGGAATTTGATCAGGACTTGTAGGTACAAGTTTAAGTTTATTAATTCGAGCTGAATTAGGTCAGCCAGGTTCATTAATTGGGGATGATCAAATTTATAATGTTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATGCCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCC | ||
| >MockIM39; KR481039;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Coleoptera,f:Chrysomelidae,g:Paria,s:Paria fragariae | ||
| GTCAACAAATCATAAAGATATTGGAACGTTATATTTTATTTTTGGAGCTTGAGCCGGAATAGTAGGAACCTCCCTAAGACTATTAATTCGAATCGAACTTGGAAATCCAGGAACTTTAATTGGAAATGATCAAATTTATAATACAATTGTAACAGCCCACGCTTTTATTATAATTTTCTTTATGGTAATACCAATTATAATTGGTGGATTTGGTAATTGATTAGTACC | ||
| >MockIM40; KM577144;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Blattodea,f:Blattidae,g:Periplaneta,s:Periplaneta fuliginosa | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATACTTCATTTTTGGTGCTTGATCAGGTATAGTAGGAACATCATTGAGAATATTAATTCGTGCTGAGCTTGGTCAACCCGGTTCACTAATTGGAGATGATCAAATTTATAATGTGATTGTAACTGCACATGCTTTCATTATAATTTTCTTTATAGTAATACCAATTATAATTGGTGGATTTGGTAATTGATTAGTACC | ||
| >MockIM42; tax=k:Animalia,p:Arthropoda,c:Arachnida,o:Opiliones,f:Phalangiidae,g:Phalangium,s:Phalangium opilio | ||
| GTCAACAAATCATAAAGATATTGGTACAATATACATAATTTTTGGGATATGGGCTGCAATAATTGGGACAGCCCTTAGTATACTAATCCGAGCTGAATTAGGACAACCTGGGTCAATAATAAATGATGATCAAATTTATAATGTTATTGTAACTGCCCATGCCTTTGTTATAATTTTCTTTATAGTAATACCTATTATAATTGGGGGATTTGGAAACTGATTAGTCCC | ||
| >MockIM44; JF867722;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Diptera,f:Chironomidae,g:Procladius,s:Procladius sp 1ES | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGTGCATGAGCCGGTATAGTAGGTACCTCCCTTAGTATCTTAGTACGGGCTGAATTAGGACATCCAGGAGCATTAATTGGTGATGATCAAATTTATAATGTAATTGTTACTGCTCACGCTTTTGTAATAATTTTTTTTATAGTTATACCTATTTTAATTGGTGGGTTTGGAAATTGATTAGTTCC | ||
| >MockIM46; HM433586;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Coleoptera | ||
| GTCAACAAATCATAAAGATATTGGAACATTATATTTTTTGTTCGGTAGTTGAGCAGGAATAGTAGGAACATCATTAAGATTACTAATCCGTGCTGAACTAGGAAACCCCGGATCTTTAATTGGTGATGATCAAATTTATAATGTAATTGTAACAGCACATGCTTTCATTATGATTTTTTTCATAGTTATACCAATTATGATTGGTGGATTTGGAAATTGACTTGTACC | ||
| >MockIM47; KM535466;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Orthoptera,f:Tettigoniidae,g:Scudderia,s:Scudderia curvicauda | ||
| GTCAACAAATCATAAAGATATTGGAACATTATACTTCATTTTTGGAGCTGAGCTGGAATAGTAGGTACATCCTTAAGACTACTTATTCGAGCCGAACTAGGGCAACCAGGATATCTAATTGGTGATGATCAAATTTATAACGTTATTGTAACTGCTCATGCATTTGTAATAATCTTCTTCATGGTTATACCTATCATAATTGGAGGATTTGGTAATTGACTAGTACC | ||
| >MockIM49; KJ787108;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Blattodea,f:Ectobiidae,g:Supella,s:Supella longipalpa | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATACTTCGTTTTTGGTGCATGATCAGGGATAGTAGGAACTTCATTAAGTATATTAATTCGCACCGAATTAAATCAACCTGGATCCTTAATTGGAGATGACCAAATCTATAATGTAATTGTTACAGCTCATGCTTTTGTCATAATCTTTTTCATAGTAATACCAATTCTTATCGGAGGATTCGGGAATTGATTAGTTCC | ||
| >MockIM52; tax=k:Animalia,p:Arthropoda,c:Insecta,o:Orthoptera,f:Tettigoniidae | ||
| GTCAACAAATCATAAAGATATTGGAACCTTGTATTTCATTTTTGGAGCATGGGCAGGTATAGTTGGTACATCTTTAAGTTTACTGATTCGAGCTGAGCTAGGGCAACCAGGTTACTTAATTGGAGATGACCAAATTTATAATGTAATTGTTACTGCTCATGCTTTTGTAATAATTTTCTTTATAGTAATACCTATTATAATTGGAGGTTTTGGAAATTGATTAGTCCC | ||
| >MockIM53; HM436311;tax=k:Animalia,p:Arthropoda,c:Insecta,o:Lepidoptera,f:Crambidae,g:Udea,s:Udea rubigalis | ||
| GTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACATCTTTAAGTTTATTAATTCGAGCTGAATTAGGAAATCCAGGTTCATTAATTGGTGATGATCAAATTTATAATACTATTGTAACAGCCCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAATTCC |
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| Taxonomy mock.IM4p4L1 | ||
| MockIM3 0.0417 | ||
| MockIM4 0.0417 | ||
| MockIM5 0.0417 | ||
| MockIM7 0.0417 | ||
| MockIM10 0.0417 | ||
| MockIM15 0.0417 | ||
| MockIM16 0.0417 | ||
| MockIM20 0.0417 | ||
| MockIM21 0.0417 | ||
| MockIM23 0.0417 | ||
| MockIM27 0.0417 | ||
| MockIM28 0.0417 | ||
| MockIM29 0.0417 | ||
| MockIM32 0.0417 | ||
| MockIM33 0.0417 | ||
| MockIM39 0.0417 | ||
| MockIM40 0.0417 | ||
| MockIM42 0.0417 | ||
| MockIM44 0.0417 | ||
| MockIM46 0.0417 | ||
| MockIM47 0.0417 | ||
| MockIM49 0.0417 | ||
| MockIM52 0.0417 | ||
| MockIM53 0.0417 |
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let's call this mock-29 (to keep consistent)