Table 1.
Currently available pipeline/software for automated NGS‐based HIVDR data analysis
| Pipeline/software | Reference information | Resources | Technical characteristics | HIV drug resistance | HIVDR data analysis features | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| URL | Yearc | Costd | Timee | Bioinformatic IT needsf | Compatible NGS platform | Cloud based | Web interface | Designed for HIVDR | Ref DB and algorithmg | Output (nt/aa)h | QA checks[Link] | InDelj | |
| V‐Phaser 2 40 | https://www.broadinstitute.org/viral‐genomics/v‐phaser‐2 | 2013 | Free | N/A | Yes | N/A | No | No | No | No | csv/csv | E | Yes |
| ShoRah 41 | https://github.com/cbg‐ethz/shorah | 2013 | Free | N/A | Yes | N/A | No | No | No | No | csv/N/A | E | N/A |
| VirVarSeq 42 | https://sourceforge.net/projects/virtools/ | 2015 | Free | N/A | Yes | Illumina | No | No | No | No | fasta/csv | Q/E | Yes |
| MinVar 43 | https://ozagordi.github.io/MinVar/ | 2016 | Free | <1 hour | Yes | Illumina | Yesk | No | Yes | HIVdb | vcf/csv | Q | Yes |
| V‐pipe | https://cbg‐ethz.github.io/V‐pipe/ | 2017 | Free | N/A | Yes | Illumina | No | No | No | No | fasta/csv | Q | Yes |
| Hivmmer 44 | https://github.com/kantorlab/hivmmer | 2017 | Free | <1 hour | Yes | Illumina | No | No | Yes | No | csv/csv | L | Yes |
| Geno2Pheno[ngs‐freq]45 a | http://ngs.geno2pheno.org/ | 2018 | Free | <1 minute | Yes | N/A | No | Yes | Yes | g2p[res] | fasta/csv | N/A | Yes |
| MiCallb | https://github.com/cfe‐labMiCall | 2016 | Free | <1 hour | No | Illumina | Yes | Yes | Yes | HIVdb | Csv/csv | Q/E | Yes |
| HyDRA | https://hydra.canada.ca | 2016 | Free | <1 hour | No | Illumina Ion Torrent | No | Yes | Yes | HIVdb | fasta,vcf/aavf | Q/E | Yes |
| PASeq.org | https://www.paseq.org | 2016 | Free | <1 hour | No | Illumina | Yes | Yes | Yes | HIVdb | fasta/csv | Q/C/A | Yes |
| DeepChek HIV 46 | https://www.ablsa.com/overview/deepchek/ | 2014 | $65l | <1 hour | No | Illumina Ion Torrent | Yes | Yes | Yes | HIVdb | csv/csv | Q | Yes |
| Smart GeneHIV | http://www.smartgene.com/mod_ngs.html | 2016 | N/A | N/A | No | N/A | No | Yes | Yes | HIVdb | N/A | N/A | Yes |
| Vela sentosa HIV 47 | http://www.veladx.com/HIV.html | 2016 | $200m | N/A | No | Ion Torrent | No | Yes | Yes | HIVdb | fasta/csv | Q | Yes |
| Hyrax Exatype | https://exatype.com/ | 2018 | N/A | <1 hour | No | Illumina IonTorrent | Yes | Yes | Yes | HIVdb | fasta/csv | Q | Yes |
The pipelines/software are categorized as: (1) freely available software for bioinformaticians (top block); (2) freely available software suitable for non‐bioinformaticians (middle block); and (3) commercial software (bottom block). Within each block, the chronological order was followed. N/A, Information not available or not applicable. NGS, next‐generation sequencing; HIVDR, HIV drug resistance.
aGeno2pheno[ngs‐freq] pipeline can only use a codon frequency table as an input which needs to be obtained separately; bpending approval and release on Illumina BaseSpace Sequence Hub. For early access, please micalldev@cfenet.ubc.ca; cyear of publication/public availability; dapproximate per sample cost of bioinformatic data analysis only; etime range for single sample data analysis (data transfer time excluded); frefers to the need of on‐site computational infrastructure or expert staff; gRef DB and algorithm: reference HIV resistance database and/or algorithms for HIV resistance interpretation (HIVdb: Stanford HIV Database); g2p[res] refers to the Geno2pheno[resistance] statistical engine; houtput: format of output files reporting nucleotide (nt) and amino acid (aa) variations; iQA check strategies incorporated for NGS read quality assurance (Q: Quality Control; C: Contamination Control; E: Sequencing Error Model; L: Alignment Quality Filter; A: ApoBEC Hypermutation Detection); jindels are recognizable by default but no codon‐aware strategies are implemented for reporting insertion/deletion mutations specifically associated to HIV resistance; kcan be ported to Cloud; lcost based on general access through Illumina basespace; mapproximate cost of whole sample analysis (sample preparation, sequencing, data analysis).