Compare sequences (new assembly vs. good one), looking for frameshift mutations

[jessMaia]

• Download all C. albicans genomes
• Make all into Blastdb (GBD)
• Download all proteins from C. albicans refseq (P)
• tBlasTn all (P) into all (GBD)
• Look for frameshift mutations

[cmball1]

Downloaded all C. albicans genomes with:

wget `esearch -db assembly -query "Candida Albicans[Organism] AND latest[filter]" | \
efetch -format docsum | \
xtract -pattern DocumentSummary -element FtpPath_GenBank | \
awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}'`

After installing EDirect Utilities modeling the command above from the EDirectCookbook

[cmball1]

• Download all C. albicans genomes Use src/get_genome_assemblies.sh or workflow/esearch_download.cwl

• Make into Blastdb

  docker run -v <local-dir>:<docker-dir> assemblyrepair:latest \
  makeblastdb -in 'GCA_000149445.2_ASM14944v2_genomic.fna GCA_000775455.1_Cand_albi_L26_V2_genomic.fna GCA_000182965.3_ASM18296v3_genomic.fna GCA_000775465.1_Cand_albi_P34048_V1_genomic.fna GCA_000447455.1_Cand_albi_A123_V1_genomic.fna GCA_000775505.1_Cand_albi_P57055_V1_genomic.fna GCA_000447475.1_Cand_albi_A92_V1_genomic.fna GCA_000775525.1_Cand_albi_P75063_V1_genomic.fna GCA_000447495.1_Cand_albi_A203_V1_genomic.fna GCA_000784495.1_Cand_albi_P76067_V1_genomic.fna GCA_000447515.1_Cand_albi_A67_V1_genomic.fna GCA_000784505.1_Cand_albi_P76055_V1_genomic.fna GCA_000447535.1_Cand_albi_A48_V1_genomic.fna GCA_000784515.1_Cand_albi_P37039_V1_genomic.fna GCA_000447555.1_Cand_albi_CHN1_V1_genomic.fna GCA_000784525.1_Cand_albi_P60002_V1_genomic.fna GCA_000447575.1_Cand_albi_A20_V1_genomic.fna GCA_000784575.1_Cand_albi_P75010_V1_genomic.fna GCA_000447595.1_Cand_albi_3153A_V1_genomic.fna  GCA_000784595.1_Cand_albi_P75016_V1_genomic.fna GCA_000447615.1_Cand_albi_A155_V1_genomic.fna GCA_000784615.1_Cand_albi_P78042_V1_genomic.fna GCA_000447635.1_Cand_albi_A84_V1_genomic.fna GCA_000784635.1_Cand_albi_SC5314_V4_genomic.fna GCA_000691765.1_Cand_albi_Ca529L_V1_genomic.fna GCA_000784655.1_Cand_albi_SC5314_V3_genomic.fna GCA_000773725.1_Cand_albi_P78048_V1_genomic.fna GCA_000784695.1_Cand_albi_Ca6_V2_genomic.fna GCA_000773735.1_Cand_albi_GC75_V1_genomic.fna GCA_002259805.1_ASM225980v1_genomic.fna GCA_000773745.1_Cand_albi_P37005_V2_genomic.fna GCA_002259865.1_ASM225986v1_genomic.fna GCA_000773755.1_Cand_albi_P94015_V1_genomic.fna GCA_002259875.1_ASM225987v1_genomic.fna GCA_000773805.1_Cand_albi_P57072_V1_genomic.fna GCA_002259885.1_ASM225988v1_genomic.fna GCA_000773825.1_Cand_albi_P37037_V1_genomic.fna GCA_002276455.1_ASM227645v1_genomic.fna GCA_000773845.1_Cand_albi_12C_V2_genomic.fna GCA_002835845.1_ASM283584v1_genomic.fna GCA_000774085.1_Cand_albi_P87_V2_genomic.fna GCA_002837675.1_ASM283767v1_genomic.fna GCA_000775445.1_Cand_albi_19F_V2_genomic.fna GCF_000182965.3_ASM18296v3_genomic.fna' \
  -dbtype nucl -parse_seqids -out Candina_Albicans

• Download all proteins from C. albicans refseq Use src/get_proteins.sh from data/ directory.

• tBlasTn all (P) into all (GBD)

  docker run -v <local-dir>:<docker-dir> assemblyrepair:latest \
  tblastn -db Candina_Albicans \
  -query /data/conserved_proteins.fasta \
  -out /data/conserved_proteins_tblastn-1.tsv \
  -outfmt '6 qaccver saccver pident nident positive mismatch frames qframe sframe qlen' \
  -num_threads 4