Generate ancestral linkage plots against an input assembly

Merge sorted fixmated BAM files with reference to an assembly, then optionally mark duplicates

Convert BAM files to cooler format for Hi-C analysis

Assess a genome FASTA with BUSCO using a chosen lineage and optional local lineage database path, then emit BUSCO gene coordinates as three bedGraph-style tables (Complete, Duplicated, Fragmented). Optionally bgzip/tabix those bedGraph files.

Maps Hi-C reads in unaligned CRAM format to a set of references.

Maps PacBio/ONT reads in unaligned CRAMs format to a set of references.

Align 10X data using Longranger and FreeBayes to a genome assembly and polish

Scaffold a set of assemblies using YaHS and RagTag. YaHS is used to scaffold the first provided assembly, and then RagTag is used to scaffold the remaining assemblies using the first scaffolded assembly as a reference. Finally the RagTag scaffolds are re-scaffolded using YaHS to correct errors.

Scaffold an assembly FASTA file using Hi-C contacts with YaHS.

Compress and index a Fasta file in multiple formats

Purge retained haplotypic duplications from an assembly using purge_dups.

If alternate assembly or alternate assemblies are provided, these will all be concatenated with the purged haplotigs.

Map reads from a FASTx file to a reference in chunks, outputting the alignments in BAM or PAF format. If BAM alignment is chosen, the output BAM files are merged.

Run FCS_GX to classify sequences in an assembly, parse the output files into a single CSV.

Generate a density file for a given feature type

Generate a bed file containing gaps and their length

Evaluate a number of standard metrics for a genome assembly, including basic statistics, MerquryFK for completeness/QV scores, and BUSCO

Generate BlobTK plots from a provided Blobtoolkit Dataset

Runs BUSCO with the relevant lineages

Preprocesses PacBio reads with optional LIMA demultiplexing, duplicate marking, and adapter trimming configured per input.

Build contact maps from pairs files using PretextMap, Juicertools, and Cooler

Generate the accessory files needed for pretext ingestion

Map read inputs and emit alignment and coverage bedGraph outputs

Generate a bigwig file containing repeat density graph

Identify regions of repeats in a genome

Extract the position of the repeats from a soft-masked Fasta file into a BED file, and compress and index it with tabix.

Run telomere/findtelomere on an assembly and motif string; optionally bgzip/tabix strand BED (*.fwd.telomere.bed, *.rev.telomere.bed) and windows files (*.windows or *.fwd.windows / *.rev.windows).

Regenerate a Pretext contact map after manual curation in PretextView. Corrects the curated AGP onto the input assembly (pretext2asm), remaps Hi-C contacts with juicerc, builds a pairs file (pretext/makepairs), and runs pretextmap.