vimalinx/bio-agent - Seite 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.

Quellsprache: Englisch

expand-current

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

Quellsprache: Englisch

export2sam-pl

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

Quellsprache: Englisch

extract-exons-py

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

Quellsprache: Englisch

extract-splice-sites-py

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

Quellsprache: Englisch

fasta-from-bed

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

Quellsprache: Englisch

fasta-sanitize-pl

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

Quellsprache: Englisch

fasterq-dump

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

feature-counts

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

Quellsprache: Englisch

fill-aa

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

Quellsprache: Englisch

fill-an-ac

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

Quellsprache: Englisch

fill-fs

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

Quellsprache: Englisch

fill-ref-md5

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

Quellsprache: Englisch

filter-columns

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

Quellsprache: Englisch

filter-genbank

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

Quellsprache: Englisch

filter-record

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

Quellsprache: Englisch

filter-stop-words

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

Quellsprache: Englisch

find-in-gene

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

flatten-gtf

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

Quellsprache: Englisch

fsa2xml

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

fuse-segments

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

Quellsprache: Englisch

gbf2facds

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

Quellsprache: Englisch

gbf2fsa

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

Quellsprache: Englisch

gbf2info

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

gbf2tbl

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

Quellsprache: Englisch

gbf2xml

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

gene2range

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

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`.

Quellsprache: Englisch

get-species-taxids-sh

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

Quellsprache: Englisch

gff-sort

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

Quellsprache: Englisch

gff2gff-py

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

Quellsprache: Englisch

gff2gff

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

Quellsprache: Englisch

gff2xml

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

Quellsprache: Englisch