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Updates to V-pipe's entry #20

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Updates to V-pipe's entry #20

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57d3d53
Updates to V-pipe's entry
DrYak Mar 28, 2022
6c6aa5f
Update V-pipe's primer trimming
DrYak Oct 3, 2022
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2 changes: 1 addition & 1 deletion workflow-overview.md
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Expand Up @@ -17,7 +17,7 @@
| SIGNAL | [Published](https://pubmed.ncbi.nlm.nih.gov/32824272/) | 15.08.20 | [link](https://github.com/jaleezyy/covid-19-signal) | Yes | Snakemake | Illumina | No | Yes | trim-galore | BWA-MEM vs composite host and viral reference | iVar | \- | \- | freeBayes, iVar | freeBayes, iVar, breseq | Pangolin, Nextclade | Yes (user defined) | Yes | Yes | Integrates with [ncov-tools](https://github.com/jts/ncov-tools/) for additional QC |
| Snakelines | [Published](http://ceur-ws.org/Vol-2962/paper15.pdf) | 24.09.21 | [link](https://github.com/jbudis/snakelines) | No | Snakemake | Illumina, (Nanopore) | Yes | Yes | cutadapt | Bowtie2 | cutadapt | \- | \- | bcftools | BCFtools, GATK | Pangolin | Yes, 3 bp | | Yes | SnakeLines is intended for the wide range of genomic analysis. The cited publication describes only a specific pipeline for SARS-CoV-2 Variant Detection. Overall, the SnakeLines offers [much more](https://arxiv.org/abs/2106.13649). |
| TAR-VIR | [Published](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2878-2) | 04.06.19 | [link](https://github.com/chjiao/TAR-VIR) | No | C++, Python | Illumina | No | Yes | \- | \- | \- | PEHaplo | \- | \- | \- | \- | \- | \- | \- | assembly with partial or not complete reference genomes, full haplotype reconstruction |
| V-pipe | [Published](https://doi.org/10.1093/bioinformatics/btab015) | 20.01.21 | [link](https://github.com/cbg-ethz/V-pipe) | No | Snakemake | Illumina | Yes | Yes | PRINSEQ | \- | \- | Vicuna, SAVAGE | \- | samtools, bcftools, ConsensusFixer | ShoRAH 2, LoFreq | \- | bcftools consensus | \- | Yes | for any virus, full haplotype reconstruction |
| V-pipe | [Published](https://doi.org/10.1093/bioinformatics/btab015) | 20.01.21 | [link](https://github.com/cbg-ethz/V-pipe) | No | Snakemake | Illumina | Yes | Yes | PRINSEQ | for public db uploads: BWA | iVar, samtools | Vicuna, (planned: SAVAGE) | \- | samtools+bcftools, smallgenomeutilities, ngshmmalign | ShoRAH 2, LoFreq | cojac | bcftools consensus, smallgenomeutilities | external scripts, matcher, smallgenomeutilities' frameshift_deletions_checks | Yes | for any virus, full haplotype reconstruction, selectable aligner, benchmarking mode, official SIB (Elixir Swiss node) software resource with long-term support |
| VEGA | [Published](https://peerj.com/articles/12129/) | 06.09.21 | [link](https://github.com/pauloluniyi/VGEA) | No | Snakemake | | | | fastp | BWA | \- | IVA | shiver/SeqKit | \- | \- | \- | \- | \- | MultiQC | |
| VIRify | Unpublished | | [link](https://github.com/EBI-Metagenomics/emg-viral-pipeline) | No | Nextflow, CWL | | No | No | TrimGalore | TrimGalore | TrimGalore | rnaSPAdes, MEGAHIT, metaSPAdes | \- | \- | \- | \- | \- | \- | | |
| ViPR | Unpublished | | | | | | | | | | | | | | | | | | | |
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