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.

slop-bed

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

snp2hgvs

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

snp2tbl

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

soap2sam-pl

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

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.

sort-by-length

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

sort-table

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

sort-uniq-count-rank

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

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.

spdi2tbl

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

split-at-intron

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

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.

star-avx2

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

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.

star

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

star-sse3

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

star-sse4-1

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

star-ssse3

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

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.

starlong-avx2

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

starlong-plain

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

starlong

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

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.

starlong-sse4-1

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

starlong-ssse3

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

subindel

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

subjunc

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

sublong

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

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.

subread-buildindex

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

subread-fullscan

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

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.

systematic-mutations

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

tabix

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

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.

tbl2prod

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

tbl2xml

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

tblastn

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

tblastn-vdb

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