vimalinx/bio-agent - 10ページ

tblastx

Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.

原文の言語: 英語

test-edirect

Use when smoke-testing an Entrez Direct installation with the bundled long-form example suite or the focused `-test` trace mode.

原文の言語: 英語

test-eutils

Use when probing NCBI E-utilities reachability or endpoint health with the bundled `-alive`, `-all`, or per-endpoint diagnostic checks.

原文の言語: 英語

test-pcre

Use when testing or benchmarking PCRE2 regular expressions with the local `test_pcre` / `pcre2test` executable.

原文の言語: 英語

test-pmc-index

Use when validating a local PMC archive/index configured through `EDIRECT_LOCAL_ARCHIVE` by round-tripping random PMC records through `xfetch` and `xsearch`.

原文の言語: 英語

test-pubmed-index

Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.

原文の言語: 英語

toml2xml

Use when converting TOML configuration or metadata files into XML for downstream EDirect or XML-based processing.

原文の言語: 英語

transmute-linux

Use when calling the Linux-specific compiled `transmute.Linux` binary directly for NCBI format conversion, sequence processing, or variation-processing workflows.

原文の言語: 英語

transmute

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.

原文の言語: 英語

union-bed-graphs

Use when you need to align multiple bedGraph tracks onto a shared interval segmentation so their values can be compared side by side.

原文の言語: 英語

uniq-table

Use when removing invariant columns from a tab-delimited table, especially in EDirect or bioinformatics comparison pipelines.

原文の言語: 英語

update-blastdb-pl

Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)

原文の言語: 英語

vcf-annotate

Use when annotating VCF files with custom annotations, applying filters, or modifying INFO/ID/QUAL/FILTER columns.

原文の言語: 英語

vcf-compare

Use when comparing two or more bgzipped and tabix-indexed VCF files to assess concordance of variant calls, positions, or genotypes.

原文の言語: 英語

vcf-concat

Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.

原文の言語: 英語

vcf-consensus

Use when applying VCF variants to a reference FASTA to generate a consensus sequence.

原文の言語: 英語

vcf-contrast

Use when comparing variant samples against background samples to identify unique genotypes and novel variants in VCF files.

原文の言語: 英語

vcf-convert

Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.

原文の言語: 英語

vcf-fix-newlines

Use when VCF files have inconsistent or non-native newline characters and need normalization before downstream processing.

原文の言語: 英語

vcf-fix-ploidy

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.

原文の言語: 英語

vcf-indel-stats

Use when calculating in-frame indel ratios from VCF files, optionally with exon annotations.

原文の言語: 英語

vcf-isec

Use when you need to compute intersections, unions, or complements between bgzipped and tabix-indexed VCF or tab-delimited files.

原文の言語: 英語

vcf-merge

Use when merging multiple VCF files by genomic position to create multi-sample VCFs from individual or fewer-sample VCFs.

原文の言語: 英語

vcf-phased-join

Use when joining multiple overlapping pre-phased VCF chunks into a single phased VCF using heterozygous calls from overlaps to determine correct phase.

原文の言語: 英語

vcf-query

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.

原文の言語: 英語

vcf-shuffle-cols

Use when you need to reorder sample columns in a VCF file to match the column order of a template VCF.

原文の言語: 英語

vcf-sort

Use when VCF files need sorting by chromosome and position, particularly before downstream analysis or indexing. Pipes VCF input through stdin.

原文の言語: 英語

vcf-stats

Use when computing statistics on VCF files, filtering variant data by quality or fields, or generating summary reports from gzipped VCF inputs.

原文の言語: 英語

vcf-subset

Use when subsetting VCF files by samples or filtering variant types from bgzipped VCF input.

原文の言語: 英語

vcf-to-tab

Use when converting VCF genotype data to simple tabular format for downstream analysis or reporting.

原文の言語: 英語

vcf-tstv

Use when you need to calculate the transition/transversion (Ts/Tv) ratio from VCF files for variant call quality assessment.

原文の言語: 英語

vcf-validator

Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.

原文の言語: 英語

vcftools

Use when working with Variant Call Format (VCF) files and need to filter, summarize, or manipulate variant data.

原文の言語: 英語

vcfutils-pl

Use when working with VCF file utilities from the bcftools bioconda package.

原文の言語: 英語

vrfs-variances

Use when summarizing `bcftools +vrfs`/`vrfs` `SITE` output into selected sites or variance vectors from a subset of loci.

原文の言語: 英語

wgsim-eval-pl

Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations.

原文の言語: 英語

wgsim

Use when simulating paired-end short reads from a reference FASTA for testing, benchmarking, or pipeline validation

原文の言語: 英語

window-bed

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.

原文の言語: 英語

window-maker

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.

原文の言語: 英語

windowmasker-2-2-22-adapter-py

Use when adapting or converting WindowMasker output files for compatibility with different BLAST pipeline versions or formats.

原文の言語: 英語