vimalinx/bio-agent - Page 4

expand-cols

Use when you need to expand comma-separated values in file columns into individual lines, replicating each line for every value in the specified columns.

expand-current

Use when expanding and rebuilding the local EDirect PubMed `Current` archive plus its derived index layers.

export2sam-pl

Use when converting legacy Illumina GERALD export files into SAM for downstream alignment analysis.

extract-exons-py

Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or transcriptome analysis.

extract-splice-sites-py

Use when extracting splice junction sites from GTF annotation files for HISAT2 genome indexing or RNA-seq alignment workflows.

fasta-from-bed

Use when extracting DNA or RNA sequences from a FASTA file using coordinate ranges from BED, GFF, or VCF files.

fasta-sanitize-pl

Use when sanitizing FASTA or FASTQ record names so they conform to SAM-compatible reference / read-name character rules.

fasterq-dump

Use when extracting FASTQ or FASTA files from NCBI SRA run accessions, especially after staging runs locally with prefetch.

fastp

Use when processing raw FASTQ files for quality control, adapter trimming, length or complexity filtering, polyG tail trimming, or generating QC reports before downstream analysis.

fastqc

Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.

feature-counts

Use when you need to assign aligned sequencing reads to genes or genomic features for expression quantification from SAM/BAM files

fill-aa

Use when filling ancestral alleles into the INFO column of VCF files using ancestral alignment data from 1000 Genomes or similar sources.

fill-an-ac

Use when you need to populate or update AC (allele count) fields in VCF files from the vcftools suite.

fill-fs

Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.

fill-ref-md5

Use when VCF headers need reference and contig tags with MD5 checksums per VCFv4.1 specification.

filter-columns

Use when filtering or manipulating columns in tabular data files from bioinformatics workflows.

filter-genbank

Use when filtering or processing GenBank-format sequence records retrieved via NCBI Entrez Direct tools

filter-record

Use when filtering records from Entrez/NCBI data streams as part of entrez-direct workflows.

filter-stop-words

Use when processing text or queries in Entrez workflows to remove common stop words from input streams

find-in-gene

Use when filtering EDirect `GENE` XML records by strand and coordinate overlap to emit matching gene names.

flank-bed

Use when you need to create flanking intervals adjacent to BED/GFF/VCF features for promoter analysis, regulatory region discovery, or upstream/downstream sequence extraction.

flatten-gtf

Use when you need to flatten exon-like GTF/GFF features into SAF meta-features for Subread or featureCounts workflows.

fsa2xml

Use when converting FASTA sequence records into XML for downstream EDirect or XML-based sequence processing.

fuse-ranges

Use when you need to merge overlapping or adjacent strand-specific alignment ranges encoded as comma-separated `start..end` lists in EDirect tables.

fuse-segments

Use when you need to merge simple tabular start/end segments into non-overlapping intervals inside EDirect-style pipelines.

gbf2facds

Use when converting GenBank format files to FASTA coding sequences (CDS) for downstream sequence analysis.

gbf2fsa

Use when converting GenBank format (.gbf) files to FASTA format (.fsa) as part of sequence data preprocessing

gbf2info

Use when converting GenBank Flat files to structured info output for downstream parsing or analysis.

gbf2ref

Use when working with GenBank format files and need to create reference indexers for sequence data retrieval or processing within the Entrez Direct toolkit.

gbf2tbl

Use when converting GenBank format files to table format as part of the Entrez Direct toolkit from bioconda.

gbf2xml

Use when converting GenBank flatfiles into XML for downstream EDirect or XML-based sequence annotation workflows.

gen-random-reads

Use when simulating transcriptome reads from a transcript FASTA and TPM table with `genRandomReads`, or when summarizing transcript lengths before building that TPM table.

gene2range

Use when converting Entrez Gene `DocumentSummary` XML for one chromosome into sorted `GENE` interval XML.

genome-coverage-bed

Use when computing genome-wide coverage from BED/GFF/VCF or BAM files, generating coverage histograms, BedGraph tracks, or per-position depth reports.

get-overlap

Use when you need to append the overlap size or gap distance between two intervals that already appear on the same line, such as paired output from `bedtools window`.

get-species-taxids-sh

Use when resolving taxonomy names or taxids into BLAST-filterable NCBI taxonomy IDs with the NCBI helper script.

gff-sort

Use when you need to reorder GFF3 records so parent features stay ahead of children in EDirect-style annotation pipelines.

gff2gff-py

Use when converting GenBank-derived GFF into bcftools/csq-friendly Ensembl-like GFF3 with the legacy `gff2gff.py` helper.

gff2gff

Use when a GFF file needs bcftools/csq-compatible gene and transcript attributes before consequence annotation.

gff2xml

Use when converting GFF or GFF3 feature annotations into structured XML for downstream EDirect-style processing.