vimalinx/bio-agent - Seite 9

skip-if-file-exists

Use when filtering a newline-delimited list of file paths so only paths without an existing regular file continue downstream.

Quellsprache: Englisch

slop-bed

Use when you need to expand genomic intervals by adding flanking base pairs to features in BED, GFF, or VCF files.

Quellsprache: Englisch

snp2hgvs

Use when converting NCBI dbSNP docsum XML into HGVS-oriented XML records for downstream variant normalization or annotation pipelines.

Quellsprache: Englisch

snp2tbl

Use when converting NCBI dbSNP docsum XML into flat tabular rows through the bundled `snp2hgvs | hgvs2spdi | spdi2tbl` pipeline.

Quellsprache: Englisch

soap2sam-pl

Use when converting legacy SOAP aligner text output into SAM, including paired-end interpretation with `-p`.

Quellsprache: Englisch

sort-bed

Use when you need to sort BED, GFF, or VCF interval files for downstream bedtools processing, or rank records by feature size or score.

Quellsprache: Englisch

sort-by-length

Use when sorting plain text lines by character length, especially in shell pipelines where one logical item is stored per line.

Quellsprache: Englisch

sort-table

Use when sorting tab-delimited, nonblank text rows with GNU `sort` while preserving a fixed tab field separator in shell pipelines.

Quellsprache: Englisch

sort-uniq-count-rank

Use when turning repeated nonblank text lines into a frequency-ranked table, with counts sorted descending after case-insensitive grouping.

Quellsprache: Englisch

sort-uniq-count

Use when counting nonblank text lines after an internal sort, especially when you want case-insensitive grouping in a compact shell wrapper.

Quellsprache: Englisch

spdi2tbl

Use when flattening SPDI XML records into sorted, deduplicated tabular rows for downstream variant pipelines.

Quellsprache: Englisch

split-at-intron

Use when processing genomic sequences that require splitting at intron boundaries as part of Entrez Direct workflows.

Quellsprache: Englisch

star-avx

Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or processing single-cell RNA-seq data with STARsolo.

Quellsprache: Englisch

star-avx2

Use when aligning RNA-seq reads to a reference genome or generating genome indices for spliced transcript alignment

Quellsprache: Englisch

star-plain

Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or performing related operations like lift-over and BAM input processing.

Quellsprache: Englisch

star

Use when aligning spliced RNA-seq reads to a reference genome, generating genome indices, or performing splice-aware alignment for transcriptome analysis.

Quellsprache: Englisch

star-sse3

Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indexes, or performing splice junction detection.

Quellsprache: Englisch

star-sse4-1

Use when aligning RNA-seq reads to a reference genome, generating STAR genome indices, or performing splice-aware transcript alignment.

Quellsprache: Englisch

star-ssse3

Use when aligning RNA-seq reads to a reference genome or generating splice-aware genome indices for transcript alignment.

Quellsprache: Englisch

starlong-avx

Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping, or when generating STAR genome indices for long-read data.

Quellsprache: Englisch

starlong-avx2

Use when aligning long RNA-seq reads to a reference genome using the AVX2-optimized STARlong aligner for splice-aware mapping.

Quellsprache: Englisch

starlong-plain

Use when aligning long RNA-seq reads (PacBio, Nanopore) to a reference genome using splice-aware mapping with STARlong.

Quellsprache: Englisch

starlong

Use when aligning long RNA-seq reads with STARlong through the CPU-dispatch wrapper installed in this environment.

Quellsprache: Englisch

starlong-sse3

Use when aligning long RNA-seq reads to a reference genome using STARlong with SSE3 optimization, or when generating genome indices for long-read splice-aware alignment.

Quellsprache: Englisch

starlong-sse4-1

Use when aligning long RNA-seq reads to a reference genome or generating genome indexes for spliced transcript alignment

Quellsprache: Englisch

starlong-ssse3

Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping using the SSSE3-optimized STARlong binary.

Quellsprache: Englisch

subindel

Use when calling short or long indels from read alignments with the Subread `subindel` tool.

Quellsprache: Englisch

subjunc

Use when aligning RNA-seq reads to a reference genome with junction detection, including exon-exon junctions and gene fusions.

Quellsprache: Englisch

sublong

Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.

Quellsprache: Englisch

subread-align

Use when aligning RNA-seq or genomic DNA-seq reads to a reference index. Supports paired-end and single-end reads in FASTQ, FASTA, SAM, or BAM formats.

Quellsprache: Englisch

subread-buildindex

Use when building an index from a reference sequence for Subread alignment tools.

Quellsprache: Englisch

subread-fullscan

Use when scanning a reference index for all high-similarity genomic locations of one specific read sequence string.

Quellsprache: Englisch

subtract-bed

Use when you need to remove overlapping portions of one interval set from another, such as subtracting blacklist, repeat, or annotation regions from BED, GFF, VCF, or BAM-like inputs.

Quellsprache: Englisch

systematic-mutations

Use when enumerating all single-position A/C/G/T substitutions for sequence strings inside an EDirect-style text pipeline.

Quellsprache: Englisch

tabix

Use when you need to index or query tab-delimited genomic files for fast region-based retrieval.

Quellsprache: Englisch

tag-bam

Use when you need to annotate BAM alignments with a two-character tag based on overlaps with BED, GFF, or VCF annotation files, such as labeling reads by feature class or interval source.

Quellsprache: Englisch

tbl2prod

Use when converting `spdi2tbl`-style variant rows into reference and altered product sequences for coding or protein variants.

Quellsprache: Englisch

tbl2xml

Use when converting tabular text into XML for downstream EDirect or XML-based processing.

Quellsprache: Englisch

tblastn

Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.

Quellsprache: Englisch

tblastn-vdb

Use when searching protein queries against translated SRA or WGS-backed VDB databases with BLAST.

Quellsprache: Englisch