bio-agent

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.

Use when counting amino-acid letters in raw protein sequence lines inside simple EDirect text pipelines.

Use when passing legacy ViennaRNA distance-matrix data through the AnalyseDists helper for simple formatting or downstream plotting workflows.

Use when analyzing equal-length sequence sets with the legacy ViennaRNA statistical-geometry, clustering, or distance-matrix utility driven from stdin.

Use when you need to annotate regions in a target TSV/BED file with information from overlapping regions in a source file, transfer columns between files based on genomic overlap, or filter/drop overlapping records.

Use when you need to annotate BED/GFF/VCF intervals with coverage depth and breadth from multiple feature files.

Use when maintaining a local NIH Open Citation Collection archive for offline citation-link lookups in EDirect workflows.

Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.

Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups.

Use when maintaining a local PubMed-to-PMCID postings archive for offline identifier crosswalks in EDirect workflows.

Use when maintaining a local PubMed Central full-text archive for offline PMC search or bulk processing.

Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing.

Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.

Use when inspecting shell argument tokenization by printing argv as a Go-style `[]string` literal.

Use when converting `Seq-entry` ASN.1/XML-like citation content into compact `CITATION` XML blocks for EDirect-style matching workflows.

Use when converting NCBI-style ASN.1 payloads into XML for downstream EDirect or XML-based processing.

Use when converting ViennaRNA-style sequence-plus-dot-bracket records on stdin into RNA connectivity-table output.

Use when converting BAM alignment files to BED6, BED12, or BEDPE format for downstream analysis or visualization.

Use when converting BAM alignment files to FASTQ format, including paired-end data requiring separate or interleaved output.

Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling.

Use when converting BED/GFF/VCF feature records to BAM format for visualization or downstream analysis.

Use when you need to generate an IGV batch script for taking snapshots at loci defined in BED, GFF, or VCF files, especially for repeatable visual review of many regions.

Use when you need to explode BED12 transcript or block annotations into one BED6 interval per block, such as converting multi-exon records into simple exon intervals for downstream interval analysis.

Use when converting BEDPE (or BED/GFF/VCF) feature records to BAM format for downstream analysis.

Use when performing genome arithmetic on interval files (BED, BAM, BEDGRAPH), including intersection, merging, coverage, format conversion, or sequence extraction.

Use when extracting the inclusive tabular block between two gene-name rows from a first-column gene list or interval table.

Use when you need to compress or decompress files using BGZF (Blocked GNU Zip Format), create BGZF indexes for random access, or prepare bioinformatics files for tabix indexing.

Use when you need a workspace-level entry point to choose among the installed bioinformatics CLIs and repo-backed AI/bio projects in this environment.

Use when working from the local Biomni repository to run agent-style biomedical tasks or inspect Biomni's biomedical tool modules and examples.

Use when you need to reformat BLAST archive files into different output formats (tabular, HTML, custom) without re-running the BLAST search.

Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling.

Use when creating BLAST database aliases, converting GI files to binary format, or aggregating multiple BLAST databases into a single virtual database.

Use when verifying integrity and validity of BLAST databases before using them in search pipelines or troubleshooting database corruption issues.

Use when retrieving sequences or metadata from local BLAST databases, looking up entries by identifier or taxonomy, or inspecting database contents.

Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.