Open nekrut opened 4 years ago
Dear all,
The list of studies that have sequenced HIV-1 pol using Illumina is
Author (Yr) | Title | # Samples1 | Genes | VL2 | Region | ARV status | Subtypes3 | Data Source4 |
---|---|---|---|---|---|---|---|---|
Avila-Rios (2016)[18] | HIV Drug Resistance in AntiretroviralTreatment-Naïve Individuals in the LargestPublic Hospital in Nicaragua, 2011-2015 | 255 | PR/RT | Yes | Nicaragua | Naive | B (99.6%) | SRA |
Moscona (2017)[14] | Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014 | 78 | PR (76); RT (77); IN (30) | No | Israel | Naïve | B (59%); C (22%); A (14%) | SRA |
Huber (2016)[19] | MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing | 33 | PR/RT (33); IN (13) | Yes | Switzerland | NA | B (67%), A (9%), C (9%), CRF02_AG (9%) | Zenodo |
Nguyen (2018)[15] | Prevalence and clinical impact of minority resistant variants in patients failing an integrase inhibitor-based regimen by ultra-deep sequencing | 134 | IN | No | France | Treated | B (60%), CRF02_AG (26%) | SRA |
Dalmat (2018)[20] | Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors | 112 | PR (93); RT (94); IN (38) | No | U.S. | Treated | B (95%), C (4%), D (1%) | SRA |
Jair (2019)[13] | Validation of publicly-available software used in analyzing NGS data for HIV-1 drug resistance mutations and transmission networks in a Washington, DC, cohort. | 42 | PR (34), RT (41), IN (33) | No | U.S. | Treated | B (98%), CRF02_AG (2%) | SRA |
Ode (2015)[16] | Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq | 92 | PR/RT/IN | Yes | Japan | Treated | B (61%), CRF01_AE (11%), C (11%), CRF02 (9%) | SRA |
Telele (2019)[17] | Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing. | 109 | PR/RT/IN | No | Ethiopia | Naive | C (99%), D (1%) | SRA |
Here is an outline of a workflow that needs to be enabled in Galaxy to allow variant calling on HIV-1 datasets
PRJNA517147
fastqc
andmultiqc
trim_galore
samtools depth
and visualize using Jupyter or Galaxy's built in visualization capabilitiesFreebayes
(Freebayes hangs on datasets where coverage if too high). The downsampling is tricky and would be a good test of new workflow functionality as it will require:samtools depth
samtools depth
compute median depth per sample. This will give one number per sample.F = 1/(median_depth_for_given_sample/1000)
. The downsampling is done usingsamtools view -s
F < 1
. IfF >= 1
no downsampling is necessarybcftools norm
bcftools query
. Here galaxy wrapper for this tools will need to have access to VCF metadata to allow field selection