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Comparison of SARS-CoV-2 Workflow Features

Workflow Status Publishing Date Source SARS-CoV-2 Exclusive Framework / Library Seq. Technology Can Process Shotgun Data Can Process Amplicon Data Read Filtering Contamination Removal Primer Trimming De Novo Assembly Scaffolding Consensus / Reference Assembly Variant Calling / Annotation Lineage Calling Low Coverage Masking Indication of Quality GUI / Report Comments
ARTIC fieldbioinformatics Unpublished link Yes Bash Nanopore No Yes Guppyplex - Custom script - - bcftools consensus medaka consensus, medaka snp, medaka variant, nanopolish variants, longshot - Custom script - State of the Art. Works with any ONT amplicon-based viral sequencing given a bed file and a reference.
C-VIEW Unpublished link AWS Illumina samtools samtools iVar - - Yes Pangolin
Genome Detective Published 16.08.21 link No Illumina, Nanopore Yes No Trimmomatic Yes - SPAdes, metaSPAdes Yes Yes - Yes Webapp
HAPHPIPE Published 03.07.20 link No Python Illumina Yes No Trimmomatic - - SPAdes MUMMER 3+ Bowtie2 - - -
HAVoC Published 17.07.21 link Yes Shell Illumina Yes No fastp, Trimmomatic - - - - bcftools/samtools LoFreq Pangolin BED-tools - -
IDseq Published 15.08.20 link No Illumina Yes No Trimmomatic, PriceSEQ, CD-HIT- DUP + - SPAdes - - - - - - Yes
IPD 2.0 Published 13.05.21 link No Python Illumina, Nanopore Yes No fastp, PoreChop, NanoFilt + - Megahit - - VarScan2, LoFreq, freebayes, Medaka, SnpEff Euclidean Distance based with data from GISAID - - Yes
LABRADOR Published 19.11.21 No Trimmomatic BWA - Megahit - - - - - - Yes
LAZYPIPE Published 02.12.20 link No Perl, R Illumina Yes No Trimmomatic, fastp + - Megahit, Velvet, SPAdes + - - - - Yes Environmental
PiGx Preprint 02.12.21 link Yes Snakemake PRINSEQ Yes LoFreq, VEP - - - Yes Environmental
RECoVERY Preprint 05.12.21 link Yes Galaxy Illumina, Nanopore Trimmomatic Bowtie2 - - - iVar iVar, SnpEff - - - -
SARS2seq Unpublished link Yes Python, Snakemake Illumina, Nanopore, IonTorrent Yes Yes fastp minimap2 AmpliGone - - TrueConsense TrueConsense Pangolin, NextClade TrueConsense - MultiQC, Amplicon Coverage
SIGNAL Published 15.08.20 link 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 for additional QC
Snakelines Published 24.09.21 link 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.
TAR-VIR Published 04.06.19 link No C++, Python Illumina No Yes - - - PEHaplo - - - - - - - assembly with partial or not complete reference genomes, full haplotype reconstruction
V-pipe Published 20.01.21 link No Snakemake Illumina Yes Yes PRINSEQ - - Vicuna, SAVAGE - samtools, bcftools, ConsensusFixer ShoRAH 2, LoFreq - bcftools consensus - Yes for any virus, full haplotype reconstruction
VEGA Published 06.09.21 link No Snakemake fastp BWA - IVA shiver/SeqKit - - - - - MultiQC
VIRify Unpublished link No Nextflow, CWL No No TrimGalore TrimGalore TrimGalore rnaSPAdes, MEGAHIT, metaSPAdes - - - - - -
ViPR Unpublished
ViReflow Unpublished link No AWS, Reflow Illumina, Nanopore Yes Yes fastp, PRINSEQ - iVar, pTrimmer coronaSPAdes, metaviralSPAdes, rnaviralSpades, MEGAHIT, minia, and Unicycler - bcftools consensus FreeBayes, iVar Variants, LoFreq Pangolin, VirStrain bcftools consensus - Yes Usable for any virus. Provides dynamic compute resource allocation (e.g. running ViReflow with 100 vs. 1,000 samples is identical from the user's perspective, but AWS resources will automatically be scaled accordingly)
nf-core/viralrecon Unpublished (nf-core is published) link No Nextflow Illumina, Nanopore Yes Yes fastp, artic guppyplex Kraken2 iVar, Cutadapt SPAdes (all relevant modes), Unicycler, minia ABACAS iVar, bcftools, artic minion iVar, BCFTools, artic minion, SnpEff, SnpSift Pangolin, nextstrain samtools, custom script Yes MultiQC Flexible, portable and community driven pipeline tested on various infrastructures including the Cloud
ViraPipe Published 02.11.17 link No Spark - - - Megahit - - - - - - -
VirusLab Published 06.11.21 - No Illumina, Nanopore - - ARTIC/Galaxy SnpEff Pangolin - - Webapp
bjorn Unpublished link Yes Snakemake, Bash No No - - - - - - - - - - - A pipeline for counting SARS-CoV-2 mutations from a set of sequences.
nCoV_minipipe, CovPipe Referenced link No Snakemake Illumina, (Nanopore) Yes Yes fastp Kraken2 bamClipper - - bcftools consensus freebayes, bcftools, SNPeff Pangolin Yes Yes Yes
ncov2019-artic-nf Unpublished link Yes Nextflow Illumina, Nanopore Yes Yes Nanopolish - iVar - - iVar iVar - Yes Yes -
poreCov Published 28.07.21 link Yes Nextflow Nanopore No Yes NanoPlot, pycoQC Yes ARTIC - - ARTIC nextstrain Pangolin, nextstrain ARTIC(< 20) ARTIC Yes

Interpretation of Features

  • Workflow: The name of the workflow.
  • Status: If the workflow was published or not. If it was published, it should contain a link to the publication.
  • Publishing Date: If the workflow was published, the date of publication.
  • Source: Link to the source code.
  • SARS-CoV-2 Exclusive: If the workflow only processes SARS-CoV-2 samples.
  • Framework / Library: Which framework or library is used for the implementation of the workflow.
  • Seq. Technology: Which sequcencing technology/technologies can be processed with the workflow.
  • Can Process Shotgun Data: If the workflow can process shotgun data.
  • Can Process Amplicon Data: If the workflow can process amplicon data.
  • Read Filtering: Which tool the workflow uses for read filtering.
  • Contamination Removal: Which tool is used for contamination removal (e.g. for reads originating from a humans genome).
  • Primer Trimming: Which tool the workflow uses for amplicon primer trimming.
  • De Novo Assembly: Which tool the workflow uses for de novo assembly.
  • Scaffolding: Which tool the workflow uses for scaffolding.
  • Consensus / Reference Assembly: Which tool the workflow uses for consensus assembly.
  • Variant Calling / Annotation: Which tool the workflow uses for variant calling and/or annotation.
  • Lineage Calling: Which tool the workflow uses for lineage calling (such as B.1.1.7, Delta, etc).
  • Low Coverage Masking: Which tool the workflow uses for low covered positions of the reconstructed genome.
  • Indication of Quality: If the workflow indicates of quality of the assembled genome, such as large share of N's or low reference similarity.
  • GUI / Report: If the workflow outputs an aggregated report. If possible, a link to the report.
  • Comments: What makes the workflow special.