diff --git a/config/README.md b/config/README.md index da69ac57..683b7891 100644 --- a/config/README.md +++ b/config/README.md @@ -52,6 +52,12 @@ Currently, the following _virus base config_ are available: - [hiv](hiv.yaml): provides HXB2 as a reference sequence for HIV, and sets the default aligner to _ngshmmalign_. - [sars-cov-2](sars-cov-2.yaml): provides NC\_045512.2 as a reference sequence for SARS-CoV-2, sets the default aligner to _bwa_ and sets the variant calling to be done against the reference instead of the cohort's consensus. In addition, a look-up for the recent versions of ARTIC protocol is provided; this makes it possible to set per-sample protocol in the sample table, and to turn on amplicon trimming (see [amplicon protocols](#amplicon-protocols)). +- [rsvb](rsvb.yaml) config file for Human respiratory syncytial virus B (RSV-B), used to process Illumina RSV samples. +- [h3n2_ha](h3n2_ha.yaml) config-file used for the analysis of H3N2 segment HA from wastewater Illumina data on SRA available through the SRA Run accession: [SRP385331](https://www.ebi.ac.uk/ena/browser/view/PRJNA856656) +- [drosophila_c_virus](drosophila_c_virus.yaml) configuration used for the analysis of drosphila C virus (DCV) Illumina samples in Lezcano et al., Virus Evolution, 2023, doi:[10.1093/ve/vead074](https://doi.org/10.1093/ve/vead074), NCBI BioProject accession number [PRJNA993483](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA993483) +- [](herpes_simplex_virus_2.yaml) config-file used for the analysis of herpes simplex virus 2 (HSV-2) Illumina samples in Lezcano et al., Virus Evolution, 2023, doi:[10.1093/ve/vead074](https://doi.org/10.1093/ve/vead074). Analysed sample is from López-Muñoz AD, Rastrojo A, Kropp KA, Viejo-Borbolla A, Alcamí A. "Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome". _Microb Genom._ 2021 Jun;7(6). Sample accession number [ERR3278849](https://www.ebi.ac.uk/ena/browser/view/ERR3278849) +- [polio](polio.yaml) config-file used for the analysis of poliovirus MinION samples. sample accession number: [ERR4027774]](https://www.ebi.ac.uk/ena/browser/view/ERR4027774) (Shaw et al., 2020, DOI: https://doi.org/10.1128/jcm.00920-20) +- [mpxv](mpxv.yaml) Monkey pox virus ### configuration manual diff --git a/config/drosophila_c_virus.yaml b/config/drosophila_c_virus.yaml index a365be09..a844cab4 100644 --- a/config/drosophila_c_virus.yaml +++ b/config/drosophila_c_virus.yaml @@ -1,3 +1,5 @@ +--- +name: Drosphila C virus # config-file used for the analysis of drosphila C virus Illumina samples # Lezcano et al., Virus Evolution, 2023, https://doi.org/10.1093/ve/vead074 # NCBI BioProject accession number PRJNA993483 @@ -8,25 +10,14 @@ general: input: reference: resources/drosphila_c_virus/NC_001834.1.fasta - datadir: resources/samples/ read_length: 100 - samples_file: samples.tsv paired: true consensus_bcftools: max_coverage: 150000 +lofreq: + consensus: false + snv: consensus: false - disk_mb: 1250 - mem_mb: 35000 - time_min: 6000 - threads: 64 - -output: - snv: true - local: true - global: false - visualization: false - diversity: false - QA: false diff --git a/config/h3n2_ha.yaml b/config/h3n2_ha.yaml index faabd98b..4ff4b9ed 100644 --- a/config/h3n2_ha.yaml +++ b/config/h3n2_ha.yaml @@ -1,3 +1,5 @@ +--- +name: Influenza A virus subtype H3N2 # config-file used for the analysis of H3N2 segment HA # config file was used to analysis wastewater Illumina data from SRA available # through the SRA Run accession: SRP385331 @@ -5,71 +7,17 @@ general: aligner: bwa primers_trimmer: samtools - threads: 6 snv_caller: lofreq - temp_prefix: ./temp preprocessor: skip input: - datadir: samples/ - samples_file: samples.tsv reference: "{VPIPE_BASEDIR}/../resources/h3n2_ha/h3n2_ha.fasta" genes_gff: "{VPIPE_BASEDIR}/../resources/h3n2_ha/gffs/h3n2_ha.gff3" paired: true read_length: 151 -output: - datadir: results/ - snv: True - local: True - global: False - visualization: False - QA: False - diversity: False - -gunzip: - mem: 100000 - -extract: - mem: 100000 - -preprocessing: - mem: 10000 - -sam2bam: - mem: 5000 - -ref_bwa_index: - mem: 65536 - -bwa_align: - mem: 40690 - threads: 8 - -bowtie_align: - mem: 12288 - threads: 6 - -coverage: - mem: 131072 - threads: 32 - time: 60 - -minor_variants: - mem: 16384 - threads: 64 - -coverage_intervals: - coverage: 0 - mem: 2000 - threads: 1 - lofreq: consensus: false snv: consensus: false - localscratch: $TMPDIR - time: 240 - mem: 1024 - threads: 64 diff --git a/config/herpes_simplex_virus_2.yaml b/config/herpes_simplex_virus_2.yaml index 26b01c09..2db31174 100644 --- a/config/herpes_simplex_virus_2.yaml +++ b/config/herpes_simplex_virus_2.yaml @@ -1,3 +1,5 @@ +--- +name: Herpes simplex Virus 2 # config-file used for the analysis of herpes_simplex_virus_2 Illumina samples # Lezcano et al., Virus Evolution, 2023, https://doi.org/10.1093/ve/vead074 # deletion analysis @@ -12,7 +14,6 @@ input: reference: resources/herpes_simplex_virus_2/MK855052.1.fasta datadir: resources/samples/ read_length: 250 - samples_file: samples.tsv paired: true consensus_bcftools: @@ -20,15 +21,3 @@ consensus_bcftools: snv: consensus: false - disk_mb: 1250 - mem_mb: 35000 - time_min: 6000 - threads: 64 - -output: - snv: true - local: true - global: false - visualization: false - diversity: false - QA: false diff --git a/config/polio.yaml b/config/polio.yaml index d3254dea..aec06b01 100644 --- a/config/polio.yaml +++ b/config/polio.yaml @@ -1,25 +1,15 @@ +--- +name: Poliovirus (MinION) # config-file used for the analysis of poliovirus MinION samples # sample accession number: ERR4027774 (Shaw et al., 2020, DOI: https://doi.org/10.1128/jcm.00920-20) general: - virus_base_config: "" aligner: minimap preprocessor: skip input: reference: resources/polio/AY560657.1.fasta - datadir: resources/samples/ - samples_file: config/samples.tsv paired: false -output: - trim_primers: false - snv: false - local: false - global: false - visualization: false - QA: false - diversity: false - minimap_align: preset: map-ont diff --git a/config/rsvb.yaml b/config/rsvb.yaml index 35a77ed5..ad1496b0 100644 --- a/config/rsvb.yaml +++ b/config/rsvb.yaml @@ -1,27 +1,21 @@ +--- +name: Respiratory Syncytial Virus B # config file for Human respiratory syncytial virus B # config file is used to process Illumina RSV samples general: - virus_base_config: "" preprocessor: "prinseq" aligner: "bwa" primers_trimmer: "samtools" input: - datadir: "samples/" - samples_file: "samples.tsv" - read_length: 251 + reference: "{VPIPE_BASEDIR}/../resources/rsvb/MT107528.1.fasta" primers_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_primers_400_V2.1.bed" inserts_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_inserts_400_V2.1.bed" - reference: "{VPIPE_BASEDIR}/../resources/rsvb/MT107528.1.fasta" + read_length: 251 -output: - datadir: "results" - trim_primers: true - snv: false - local: false - global: false -snv: - consensus: false lofreq: consensus: false + +snv: + consensus: false