Menu
Skills in this repository
SkillsMP has collected 417 skills from vimalinx/bio-agent. Open a skill to review its source and details.
vimalinx/bio-agentShowing 40 of 417 collected skills.
Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.
Use when smoke-testing an Entrez Direct installation with the bundled long-form example suite or the focused `-test` trace mode.
Use when probing NCBI E-utilities reachability or endpoint health with the bundled `-alive`, `-all`, or per-endpoint diagnostic checks.
Use when testing or benchmarking PCRE2 regular expressions with the local `test_pcre` / `pcre2test` executable.
Use when validating a local PMC archive/index configured through `EDIRECT_LOCAL_ARCHIVE` by round-tripping random PMC records through `xfetch` and `xsearch`.
Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.
Use when converting TOML configuration or metadata files into XML for downstream EDirect or XML-based processing.
Use when calling the Linux-specific compiled `transmute.Linux` binary directly for NCBI format conversion, sequence processing, or variation-processing workflows.
Use when invoking the public `transmute` wrapper for format conversion, sequence editing, or shell-level helper modes that may be intercepted before dispatch to the platform binary.
Use when you need to align multiple bedGraph tracks onto a shared interval segmentation so their values can be compared side by side.
Use when removing invariant columns from a tab-delimited table, especially in EDirect or bioinformatics comparison pipelines.
Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)
Use when annotating VCF files with custom annotations, applying filters, or modifying INFO/ID/QUAL/FILTER columns.
Use when comparing two or more bgzipped and tabix-indexed VCF files to assess concordance of variant calls, positions, or genotypes.
Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
Use when applying VCF variants to a reference FASTA to generate a consensus sequence.
Use when comparing variant samples against background samples to identify unique genotypes and novel variants in VCF files.
Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.
Use when VCF files have inconsistent or non-native newline characters and need normalization before downstream processing.
Use when VCF files have incorrect ploidy annotations for sex chromosomes or mitochondrial DNA, particularly when processing samples with known sex but mismatched genotype fields.
Use when calculating in-frame indel ratios from VCF files, optionally with exon annotations.
Use when you need to compute intersections, unions, or complements between bgzipped and tabix-indexed VCF or tab-delimited files.
Use when merging multiple VCF files by genomic position to create multi-sample VCFs from individual or fewer-sample VCFs.
Use when joining multiple overlapping pre-phased VCF chunks into a single phased VCF using heterozygous calls from overlaps to determine correct phase.
Use when extracting and formatting specific fields from compressed VCF files, querying variants by region, or generating custom tabular output with genotype and INFO data.
Use when you need to reorder sample columns in a VCF file to match the column order of a template VCF.
Use when VCF files need sorting by chromosome and position, particularly before downstream analysis or indexing. Pipes VCF input through stdin.
Use when computing statistics on VCF files, filtering variant data by quality or fields, or generating summary reports from gzipped VCF inputs.
Use when subsetting VCF files by samples or filtering variant types from bgzipped VCF input.
Use when converting VCF genotype data to simple tabular format for downstream analysis or reporting.
Use when you need to calculate the transition/transversion (Ts/Tv) ratio from VCF files for variant call quality assessment.
Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.
Use when working with Variant Call Format (VCF) files and need to filter, summarize, or manipulate variant data.
Use when working with VCF file utilities from the bcftools bioconda package.
Use when summarizing `bcftools +vrfs`/`vrfs` `SITE` output into selected sites or variance vectors from a subset of loci.
Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations.
Use when simulating paired-end short reads from a reference FASTA for testing, benchmarking, or pipeline validation
Use when you need to find features in one file that fall within a configurable window around features in another file, including strand-aware upstream and downstream proximity searches.
Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.
Use when adapting or converting WindowMasker output files for compatibility with different BLAST pipeline versions or formats.