mashID database it identify mycobacteria
收藏NIAID Data Ecosystem2026-05-01 收录
下载链接：
https://figshare.com/articles/dataset/mashID_database_it_identify_mycobacteria/25292662
下载链接
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资源简介：
db_fodler=/media/36tb/db/mashID/mycoID
# Mbovis mashID db update
https://github.com/duceppemo/mashID
# Download RefSeq -> 10719
conda activate ncbi
bash ~/prog/ncbi/refseqDownloader.sh \
-d bacteria \
-q "Mycobacterium,Mycolicibacterium,Mycolicibacter,Mycolicibacillus,Mycobacteroides" \
-u \
-f fna \
-o "$db_fodler" \
-r
conda deactivate
# Remove bad downloads -> 19
rm "${db_fodler}"/*.gz
# Remove Mycobacterium sp. -> 290
find "$db_fodler" -name "*_sp_*" -exec rm {} \;
# Derep
conda activate mashID
python ~/prog/Assembly-Dereplicator/dereplicator.py \
--distance 0.001 \
--threads $(nproc) \
"${db_fodler}"/fna \
"${db_fodler}"/fna_derep_0.001
conda deactivate
# Add bovis ref genome
conda activate ncbi
bash get_assemblies_v2.sh \
-q NC_002945.4 \
-t refseq \
-o "${db_fodler}"/fna_derep_0.001 \
-r \
-u
conda deactivate
conda activate mashID
python ~/prog/mashID/make_mashID_db.py \
-i "${db_fodler}"/fna_derep_0.001 \
-o /media/36tb/db/mashID \
-p mycobacteria_2024-02-23.msh \
-t $(nproc) \
-s 10000 \
-k 21
baseDir=/home/bioinfo/analyses/MBWGS051
python ~/prog/mashID/mashID.py \
-i "${baseDir}"/fastq \
-o "${baseDir}"mashID \
-d /media/36tb/db/mashID/mycobacteria_2024-02-23.msh \
-p 3
创建时间：
2024-02-26
