vimalinx/bio-agent - Page 2

blastn-vdb

Use when searching nucleotide sequences against SRA/VDB databases using BLAST. Invokes blastn_vdb for nucleotide-nucleotide alignment with SRA accessions.

blastp

Use when comparing protein sequences against protein databases for similarity searches, homology detection, or functional annotation.

blastx

Use when comparing translated nucleotide query sequences against protein databases to identify homologous proteins and potential protein-coding regions.

blst2gm

Use when converting compatible BLAST annotation XML/ASN streams into a compact gene-markup-style table for downstream EDirect interval helpers.

blst2tkns

Use when turning EDirect-style BLAST XML alignment blocks into a token stream for downstream shell or xtract-based parsing.

bowtie2-align-l

Use when aligning sequencing reads to a reference using Bowtie 2's large-index alignment engine.

bowtie2-align-s

Use when aligning sequencing reads (FASTQ/FASTA) to a reference genome using Bowtie 2. Supports paired-end, unpaired, interleaved, and BAM inputs with SAM output.

bowtie2-build-l

Use when building large Bowtie 2 index files from reference sequences for alignment of reads to large genomes (>4 billion bases).

bowtie2-build-s

Use when building Bowtie 2 index files from reference sequences for short-read alignment.

bowtie2-build

Use when building Bowtie 2 index files from reference FASTA sequences for subsequent read alignment with bowtie2.

bowtie2-inspect-l

Use when you need to inspect or extract information from a Bowtie 2 large index (.bt2l) file, including reference sequence names, lengths, or FASTA sequences.

bowtie2-inspect-s

Use when you need to inspect Bowtie 2 index files to extract reference sequence names, lengths, or index summary information from .bt2 files.

bowtie2-inspect

Use when you need to extract reference sequences, names, or summary information from a Bowtie2 index file.

bowtie2

Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.

bowtie2sam-pl

Use when converting legacy Bowtie text output into SAM and retaining only the best alignment per read.

bsmp2info

Use when converting BioSample `DocumentSummary` XML into a compact `BioSampleInfo` XML summary with accession, title, links, and harmonized attributes.

bwa

Use when aligning low-divergence DNA sequence reads to a reference genome

cit2pmid

Use when resolving structured citation fields or citation XML into candidate PubMed IDs with EDirect matching modes.

cleanup-blastdb-volumes-py

Use when managing BLAST database storage by removing unnecessary volume files to reclaim disk space.

closest-bed

Use when you need to find the closest genomic feature in one file for each feature in another file, including distance calculations and strand-aware lookups.

clustalw

Use when performing multiple sequence alignments on protein or nucleotide sequences, generating phylogenetic trees, or producing alignment output in various formats.

clustalw2

Use when running legacy ClustalW 2.1 multiple-sequence-alignment workflows, guide-tree calculations, or interactive alignment sessions from the command line.

cluster-bed

Use when you need to cluster overlapping or nearby genomic intervals in BED, GFF, or VCF files into groups.

color-chrs-pl

Use when rendering `bcftools +color-chrs` `.dat` output into an SVG chromosome-coloring plot, optionally with custom haplotype colors.

combine-uid-lists

Use when unioning multiple Entrez or NCBI UID files into one deduplicated numeric-sorted list.

complement-bed

Use when you need to find genomic regions NOT covered by features in a BED/GFF/VCF file, such as identifying gaps, intergenic regions, or uncovered intervals.

convert2blastmask

Use when converting lower-case masked FASTA files to masking formats compatible with makeblastdb for BLAST database preparation.

coverage-bed

Use when computing coverage depth and breadth of features from one interval file overlapping intervals in another. Applies to BED, GFF, or VCF inputs requiring overlap counts, covered bases, and coverage fractions.

csv2xml

Use when converting CSV-style tabular data into XML for downstream EDirect or XML-based processing.

ct2db

Use when converting RNA connectivity-table (`.ct`) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases.

cutadapt

Use when you need to remove adapter sequences from high-throughput sequencing reads, trim low-quality bases, or filter reads by length. Supports single-end and paired-end FASTQ/FASTA input with error-tolerant adapter matching.

datatool

Use when working with NCBI ASN.1 module files, schema exports, or ASN.1/XML conversion tasks that require the `datatool` command.

deltablast

Use when performing domain-enhanced protein sequence similarity searches to detect remote homologs using conserved domain databases.

difference-uid-lists

Use when finding the symmetric difference between two Entrez or NCBI UID files.

disambiguate-nucleotides

Use when expanding IUPAC ambiguous nucleotide strings into all concrete DNA sequences in shell or EDirect pipelines.

download-flatfile

Use when mirroring consolidated NCBI GenBank flatfile divisions into the current directory or verifying existing downloaded flatfiles.

download-ncbi-data

Use when downloading static NCBI reference datasets such as taxonomy, MeSH tree, bioconcepts, generif, journals, serials, or PMC open access files via CLI.

download-ncbi-software

Use when fetching a small set of NCBI command-line binaries (`magic-blast`, `datasets`, or `sra-toolkit`) with the bundled EDirect downloader.

download-pmc

Use when bulk-downloading PubMed Central OA tarballs across the standard PMC sections with the EDirect helper script.

download-pubmed

Use when you need to bulk-download PubMed baseline or update files from NCBI's FTP server for local offline analysis.