vimalinx/bio-agent - Page 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.

Langue du texte source : anglais

slop-bed

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

Langue du texte source : anglais

snp2hgvs

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

Langue du texte source : anglais

snp2tbl

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

Langue du texte source : anglais

soap2sam-pl

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

sort-by-length

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

Langue du texte source : anglais

sort-table

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

Langue du texte source : anglais

sort-uniq-count-rank

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

spdi2tbl

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

Langue du texte source : anglais

split-at-intron

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

star-avx2

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

star

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

Langue du texte source : anglais

star-sse3

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

Langue du texte source : anglais

star-sse4-1

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

Langue du texte source : anglais

star-ssse3

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

starlong-avx2

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

Langue du texte source : anglais

starlong-plain

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

Langue du texte source : anglais

starlong

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

starlong-sse4-1

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

Langue du texte source : anglais

starlong-ssse3

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

Langue du texte source : anglais

subindel

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

Langue du texte source : anglais

subjunc

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

Langue du texte source : anglais

sublong

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

subread-buildindex

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

Langue du texte source : anglais

subread-fullscan

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

systematic-mutations

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

Langue du texte source : anglais

tabix

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

tbl2prod

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

Langue du texte source : anglais

tbl2xml

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

Langue du texte source : anglais

tblastn

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

Langue du texte source : anglais

tblastn-vdb

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

Langue du texte source : anglais