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Yeast isolates的分析步骤

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对于kombucha的分离株混合组装后的基因组分析流程

yeast isolates的分析步骤

Funannotate分析(只做eggnog和antismash)

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#数据库建立，记得使用-w来用wget下载，不然报错
funannotate setup -d /data/Food/primary/R0987_nextgen/Erkang.Zhang/funannotate_db -w

#mask
funannotate mask -i KLI1401.fasta --cpus 12 -o KLI1401_mask.fasta

#修改序列名称，16字符之内不然下一步报错，并且记得指定--min，不然这一步报错
funannotate sort -i KLI1401_mask.fasta -o KLI1401_mask_sort.fasta  --minlen 1

#predict,--names KLI1401不然会locus_tag一样，compare时报错
funannotate predict -i KLI1401_mask_sort.fasta -o KLI1401_fun \
    --species "Brettanomyces bruxellensis" --strain KLI1401 \
    --cpus 12 --names KLI1401
########################
#运行完predict后需要使用多个工具来生成对gene的注释
########################
conda init
source ~/.bashrc
source ~/.bash_profile
#########################
conda activate eggnog

mkdir KLI1401_fun/eggnog_output

emapper.py --data_dir /data/Food/primary/R0987_nextgen/Erkang.Zhang/eggnog_db \
           -i KLI1401_fun/predict_results/Brettanomyces_bruxellensis_KLI1401.proteins.fa \
           -o KLI1401_fun/eggnog_output/KLI1401 -m diamond --cpu 16

conda deactivate
#######################
#genefinding-tool_none不然报错
conda activate antismash

antismash KLI1401_fun/predict_results/Brettanomyces_bruxellensis_KLI1401.gbk --output-dir KLI1401_fun/antismash_output \
                        --output-basename KLI1401 --cc-mibig --cb-knownclusters -t fungi \
                        --cb-general --cb-subclusters --genefinding-tool none \
                        -v --logfile KLI1401_fun/antismash_output/KLI1401_log.txt

conda deactivate
###########################可以选择不做
#conda activate funannotate

#funannotate remote -i KLI1401_fun -o KLI1401_fun/phobius_output -m phobius -e erkang.zhang@teagasc.ie

#conda deactivate
###########################

########再运行annotate，将之前的数据传过来#########
conda activate funannotate

funannotate annotate -i KLI1401_fun --species "Brettanomyces bruxellensis" \
                     -o KLI1401_fun_annotate \
                     --eggnog KLI1401_fun/eggnog_output/KLI1401.emapper.annotations \
                     --antismash KLI1401_fun/antismash_output/KLI1401.gbk --isolate KLI1401 --cpus 20


funannotate annotate -i KLI1405_fun --species "Brettanomyces bruxellensis" \
                     -o KLI1405_fun_annotate \
                     --eggnog KLI1405_fun/eggnog_output/KLI1405.emapper.annotations \
                     --antismash KLI1405_fun/antismash_output/KLI1405.gbk --isolate KLI1405 --cpus 20
                     
conda deactivate                           
##############################

#####运行compare，生成网页，有一些图可以用#############
funannotate compare -i KLI1401_fun/annotate_results/Brettanomyces_bruxellensis_KLI1401_newlocus.gbk KLI1405_fun/annotate_results/Brettanomyces_bruxellensis_KLI1405_newlocus.gbk -o funannotate_compare_KLI1401_KLI1405 --cpus 5

  • 如果predict忘了–name，可以手动修改输入给compare的gbk文件

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    sed 's/FUN_/KLI1405_/g' KLI1405_fun/annotate_results/Brettanomyces_bruxellensis_KLI1405.gbk >KLI1405_fun/annotate_results/Brettanomyces_bruxellensis_
    KLI1405_newlocus.gbk