vimalinx/bio-agent - Page 5

gm2ranges

Use when converting BLAST/genomic-map alignment summaries into compact strand-and-range tables for later interval fusion.

gm2segs

Use when converting BLASTN mRNA alignment XML into segmented interval reports and strand-overlap summaries in EDirect pipelines.

group-by

Use when you need to summarize tabular data by grouping rows on common column values and applying aggregation operations (sum, count, mean, etc.), similar to SQL GROUP BY.

guess-ploidy-py

Use when plotting `bcftools +guess-ploidy -v` output into a PNG summary of haploid, diploid, score, and site-count signals across samples.

hgvs2spdi

Use when converting EDirect HGVS XML records into NCBI SPDI XML, optionally with a precomputed accession-to-CDS-offset transform table.

hisat2-align-l

Use when aligning RNA-seq reads to a reference genome using a HISAT2 index, particularly for splice-aware alignment of transcriptomic data.

hisat2-align-s

Use when aligning RNA-seq reads to a HISAT2 index using the alignment binary directly. Supports spliced alignment with optional splice site annotation.

hisat2-build-l

Use when building large HISAT2 index files from reference sequences for RNA-seq alignment with splice-aware mapping support.

hisat2-build-s

Use when building a HISAT2 graph-based index from reference sequences for splice-aware RNA-seq alignment, optionally incorporating SNPs, haplotypes, splice sites, or exon annotations.

hisat2-build

Use when building HISAT2 index files from reference genomes for subsequent alignment with hisat2. Handles FASTA reference inputs and creates .ht2 index files.

hisat2-extract-exons-py

Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or splice-aware alignment preparation.

hisat2-extract-snps-haplotypes-ucsc-py

Use when extracting SNPs and haplotypes from UCSC SNP files for HISAT2 graph-based genome indexing.

hisat2-extract-snps-haplotypes-vcf-py

Use when extracting SNPs and haplotypes from VCF files to build variant-aware HISAT2 graph genome indexes

hisat2-extract-splice-sites-py

Use when extracting splice junctions from GTF annotation files for HISAT2 splice-aware alignment.

hisat2-inspect-l

Use when you need to inspect or extract information from HISAT2 large index files (.ht2l), including reference sequences, splice sites, SNPs, exons, or index summaries.

hisat2-inspect-s

Use when extracting metadata, reference names, SNPs, splice sites, or exon information from HISAT2 index files (.ht2).

hisat2-inspect

Use when you need to inspect HISAT2 index files, extract reference sequences, view index summaries, or retrieve SNP/splice site/exon information from a .ht2 index.

hisat2-read-statistics-py

Use when you need to compute basic read statistics (count, min/max/average length) from FASTQ/FASTA files before or after HISAT2 alignment workflows.

hisat2-simulate-reads-py

Use when simulating RNA-seq or DNA-seq reads from a reference genome and GTF annotation file, optionally incorporating SNP variants and controlling expression profiles.

hisat2

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

hmmalign

Use when aligning sequences to a profile HMM to produce multiple sequence alignments.

hmmbuild

Use when turning curated multiple-sequence alignments into profile HMM files for HMMER search or database-preparation workflows.

hmmconvert

Use when converting profile HMM files between HMMER3 ASCII or binary, legacy HMMER2, or specific 3.x text revisions.

hmmemit

Use when sampling synthetic sequences, alignments, or consensus sequences from one or more profile HMMs.

hmmfetch

Use when you need to extract specific HMM profiles from an HMM database file by name, or index an HMM file for faster lookups.

hmmlogo

Use when extracting per-position residue-height and indel-rate data from a profile HMM for sequence-logo visualization.

hmmpgmd-shard

Use when running the sharded `hmmpgmd_shard` daemon so large protein sequence databases are split across HMMER worker nodes.

hmmpgmd

Use when running HMMER master or worker daemon services that front `phmmer`, `hmmsearch`, and `hmmscan` against cached databases.

hmmpress

Use when preparing profile HMM databases for use with hmmpgmd (HMMER daemon) by creating compressed binary index files.

hmmscan

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

hmmsearch

Use when searching profile hidden Markov models against sequence databases to identify homologous sequences or protein family members

hmmsim

Use when you need to characterize score distributions of a profile HMM on random sequences, such as calibration checks, benchmarking, or filter-behavior experiments.

hmmstat

Use when you need to inspect and summarize statistics for HMM (profile hidden Markov model) files from the HMMER suite.

htsfile

Use when you need to identify, view, or copy HTS-format files (BAM, CRAM, VCF, BCF). Use for inspecting file headers or viewing textual representations of binary HTS files.

ini2xml

Use when converting INI-style configuration files into XML for downstream EDirect or XML-based processing.

interpolate-sam-pl

Use when deriving interpolated per-base coverage counts from a sorted SAM file, especially across paired-end inserts.

intersect-bed

Use when you need to find overlaps between two genomic interval files (BED, GFF, VCF, or BAM), filter features by intersection, or count/report overlapping regions between datasets.

intersect-uid-lists

Use when keeping only the Entrez or NCBI UIDs present in both of two UID files.

iqtree

Use when inferring maximum-likelihood phylogenies from aligned sequences, performing automated model selection, or assessing branch support with bootstrap or aLRT methods

iqtree3

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.