Similar projects: https://github.com/shenwei356/sun2021-cami-profiles
Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates.
Two mock communities were designed (A and B) corresponding to two contrasting situations with either low abundance of ssDNA viruses (MCA, total ssDNA ∼2% of community) or high abundance of ssDNA viruses (MCB, total ssDNA ∼66% of community)
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. 2016. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 4:e2777 https://doi.org/10.7717/peerj.2777
Phages (rank is based on NCBI taxonomy 2021-12-06)
| phage | taxid | species | genus | family |
|---|---|---|---|---|
| PSA-HM1 | 1357705 | Pseudoalteromonas phage HM1 | Myoviridae | |
| PSA-HP1 | 1357706 | Pseudoalteromonas virus HP1 | Melvirus | Zobellviridae |
| PSA-HS1 | 1357707 | Pseudoalteromonas phage HS1 | Siphoviridae | |
| PSA-HS2 | 1357708 | Pseudoalteromonas phage HS2 | Siphoviridae | |
| PSA-HS6 | 1357710 | Pseudoalteromonas phage HS6 | Siphoviridae | |
| Cba phi38:1 | 1327977 | Cellulophaga phage phi38:1 | Podoviridae | |
| Cba phi18:3 | 1327983 | Cellulophaga phage phi18:3 | Podoviridae | |
| Cba phi38:2 | 1327999 | Cellulophaga phage phi38:2 | Myoviridae | |
| Cba phi13:1 | 1327992 | Cellulophaga virus ST | Cbastvirus | Siphoviridae |
| Cba phi18:1 | 1327982 | Cellulophaga virus Cba181 | Helsingorvirus | Siphoviridae |
| phix174 | 2886930 | Escherichia virus phiX174 | Sinsheimervirus | Microviridae |
| alpha3 | 10849 | Escherichia virus alpha3 | Alphatrevirus | Microviridae |
The abundance of phages in every sample is listed in Table S2. We converted the abundance table to CAMI format, available at: https://github.com/shenwei356/roux2016-mock-virome-cami-profile
Mock communities A and B are available at: http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/DNA_Viromes_library_comparison.
the 3 different protocols are indicated with a one-letter code: "S" for A-LA, "N" for TAG, and "G" for MDA. For mock communities, replicates are indicated with a number next to the library code.
There are 16 samples in total:
MCA-G1
MCA-G2
MCA-N1
MCA-N2
MCA-S1
MCA-S2
MCA-S3
MCB-G1
MCB-G2
MCB-G3
MCB-N1
MCB-N2
MCB-N3
MCB-S1
MCB-S2
MCB-S3
But we found some name inconsistencies between the abundance table and FASTQ files. After carefully checking, we renamed samples as below:
old new
MCA-G1 MCA-G2
MCA-G2 MCA-G3
MCA-N2 MCA-N3
We manually download the paired and unpaired reads for every sample, for example:
$ ls reads/ | head -n 4
MCA-G2_GGACTCCT-GCGTAAGA_L002_R1_001_t_paired.fastq.gz
MCA-G2_GGACTCCT-GCGTAAGA_L002_R1_001_t_unpaired.fastq.gz
MCA-G2_GGACTCCT-GCGTAAGA_L002_R2_001_t_paired.fastq.gz
MCA-G2_GGACTCCT-GCGTAAGA_L002_R2_001_t_unpaired.fastq.gz
NCBI Taxonomy version: 2021-12-06
csvtk xlsx2csv gs.xlsx \
| csvtk rename2 -F -f MC* -p '(MC.) (.+) (\d)' -k method.map --key-capt-idx 2 -r '$1-{kv}$3' \
| csvtk csv2tab \
> gs.tsv
mkdir -p roux2016
csvtk headers -t gs.tsv | awk 'NR > 3' \
| rush 'csvtk cut -t -f taxid,{} gs.tsv | sed 1d > roux2016/{}.tsv'
taxver=ncbi-taxonomy-2021-12-06
taxdump=taxdump
rm roux2016/*.profile
ls roux2016/* \
| rush -v taxver=$taxver -v taxdump=$taxdump \
'taxonkit profile2cami --data-dir {taxdump} -s {%:} -t {taxver} {} -o {}.profile'
cat roux2016/*.profile > roux2016_gs.profile
# names in current taxonomy
csvtk cut -t -f 1-2 gs.tsv \
| taxonkit lineage -nrL -i 2 --data-dir taxdump/ \
| csvtk rename -t -f 3,4 -n name,rank \
> names.tsv
Families
reads=kmcp-pese
X=taxdump/
ls roux2016/*.tsv \
| rush -k \
'csvtk cut -Ht -f 1 {} \
| taxonkit reformat -I 1 -f "{f}" --data-dir taxdump \
| csvtk uniq -Ht -f 2 \
| csvtk mutate2 -Ht -e "\"{%.}\"" \
| csvtk cut -Ht -f 3,2 ' \
| csvtk add-header -t -n sample,family \
> family.gs.tsv