القائمة
Use when retrieving sequences or metadata from local BLAST databases, looking up entries by identifier or taxonomy, or inspecting database contents.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
| name | blastdbcmd |
| description | Use when retrieving sequences or metadata from local BLAST databases, looking up entries by identifier or taxonomy, or inspecting database contents. |
| disable-model-invocation | true |
| user-invocable | true |
blastdbcmd/home/vimalinx/miniforge3/envs/bio/bin/blastdbcmdmakeblastdb produced what your pipeline expects.# 1) Inspect database metadata
blastdbcmd -db proteins_db -info
# 2) Retrieve one entry in FASTA format
blastdbcmd \
-db proteins_db \
-entry XP_123456.1 \
-outfmt "%f"
# 3) Retrieve many entries from a batch file
blastdbcmd \
-db proteins_db \
-entry_batch ids.txt \
-outfmt "%f" \
-out hits.fa
# 4) Export taxonomy summary
blastdbcmd -db proteins_db -tax_info
-info first to confirm the database type and metadata.-entry or -entry_batch only if the DB was built with usable sequence IDs.-outfmt deliberately; %f is the common FASTA choice for sequence export.-tax_info rather than trying to parse raw metadata blobs.-entry, -entry_batch, -info, -metadata, and -tax_info are mutually exclusive modes.-entry all can dump an entire database, which is often much larger than expected.-parse_seqids.