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Separates a sam alignment from a heterozygous individual

Provides information about the number of scaffolds, including the N50, number of scaffolds, and distribution of lengths of assembled scaffolds.

Utilities for axt alignments

Convert axt alignments to sam format

Returns a bed file with the Score field containing the minimum distance from the end of the chromosome.

Output a subset of a bed file using score, name, position, and length

Options to alter bed formatting

Converts bedGraph to wig.

Performs comparative arithmetic operations on float values in bed files

Combines overlapping bed entries, keeping max score.

Calculates the minimum distance between beds in separate files with matching names

Given a window size (default 5000), return the number of base pairs that are in any bed region within that window

Converts a bed and fasta sequences into amino acid sequences within the bed regions

Extracts sequences from a fasta file from regions specified by an input bed

Converts bed score to wig

Returns bed file with entries annotated based on the values corresponding to the region in a wig file

Filters bedpe entries based on overlaps from the select file.

Using a four-way multiple alignment (including the reference species followed by three successive outgroups), this program calculates branch lengths in units of estimate substitutions for regions in the alignment specified by an input bed file

A tool to find variation between multiple alignment files

Concatenate multiFa alignment files by sequence.

Uses globalAlignment, affineGap (instead of constGap) to align 2 .fasta files, each with only 1 sequence, then convert cigars to ins and del beds

Determine the mutation spectrum for divergent sites in each region of an input bed file

Generates a newick tree file from an input dot format tree

Reads a newick format text file to a png for tree visualization

Computes the Dunn Index based on variable SNPs for each input bed region of a multiple alignment

Bins fastas into a minimum size group with either a single record or multiple records from a size ordered chrom.sizes file

Align two or more sequences by "chunks" of bases instead of by single bases.

Align two or more sequences by "chunks" of bases instead of by single bases.

Returns a filtered fasta based on option parameters

Returns number of mutations that separate two sequences for a given window size

Reformat the sequences in a fasta file

Returns summary statistics to standard out for an input.fa, including the counts for each base.

Make deep learning prediction TSV files from input fasta format data

Pull unique sequences from a fasta file

Returns a filtered fastq based on option parameters

Options alter fastq file formatting

Filter genotyped VCFs containing at least 3 samples with SNP regions where parental genomes are homozygous (and different) and have a clear heterozygous F1 from the parents

Finds values in a file and replaces them, processes the input as a string

Generates ideogram txt file from a bed

Filter gaf file.

geneAssignmentStats compares a bedpe containing a gene symbol in the name field to a test set of output from assignGenomeSpace command which assigns every base in the genome a closest gene either from proximity or from a 3d contact map.

Find and replace gene IDs with gene names according to an input table or preset NCBI RefSeq / ENSEMBL ID conversion tables

getPromoter will take a list of unique genes of interest and return a bed file of the promoter region proceeding the position of the TSS for each isoform by the amount specified with upstream and following the TSS by the amount specified by downstream.

GIRAF <-> GIRAF.FE conversion, for more information, see the giraf package

Returns a file of giraf alignments for a input genome graph

External sort of giraf records based on topological ordering of nodes in input graph

Align two FASTA files, each with only 1 sequence

Operates on 2 species, takes alignment maf, filters for trusted matches (s lines generated from the same chromosome in both species), and aligns the gap sequences between the trusted matches (affineGap, DefaultScoreMatrix)

View http url links and print data stream to stdout

A collection of tools that use the gonomics core library

Perform functional enrichment analysis by associating genomic regions with their nearest gene in 3d space using bedPe contact sites.

Graph-Smith-Waterman: align single or paired end fastqs

Generate unique haplotypes for provided regions from genetic variation data

Returns all regions that contact input genomic regions

A tool to find non/overlapping genomic regions

Produces a binary matrix for accessibility breadth analysis

Write out lastZ pairwise inputs using contig alignment where multiple references are being used

Lifts a compatible file format between assembly coordinates

Filter a maf file to remove entries below a score threshold

Takes pairwise alignment maf and finds insertions in species_ins not present in species_del but flanked by continuous alignments

Convert a maf alignment into a bed, where the bed score is the alignment score

Convert a maf alignment into a multiple fasta alignment

Returns summary statistics on an MCMC trace file produced by selectionMCMC

Merge two multiFa files on a shared reference.

Executes an external merge sort of the input file based on desired sort criteria

Provides human-readable multiple alignments for all entries in a bed file

Provides human-readable multiple alignment from a given multiFa

Performs velocity and acceleration on a four way multiple alignment in multiFa format

Pull sub-sequence from multiple Fasta alignment for each entry

Removes all columns in a multi fasta alignment that are not variable

Scan multiple Fasta alignment for a user-specified pattern (N for now) and report bed regions in reference sequence coordinates

Convert a pairwise multiFa format alignment to a chain file.

Generates a VCF file from an input pairwise or three-way multiFa alignment with the first entry as the reference

Returns the p-value of enrichment and depletion for overlaps between the elements in two input files

A collection of tools for manipulating pFasta files

Count bases from sequencing data

Returns a tab separated list of function evaluations for plotting functions

Generates a binary input matrix for PCA

Pseudorandomly selects variants from an input VCF file

A collection of tools for manipulating position matrices

Find corresponding orthologous transcription start

Returns pseudorandomly generated DNA sequences in fasta format

Reconstruct ancient sequences using extant genomes and a newick tree with branch lengths

Reference-based diploid assembly of aligned short reads

Generates a fasta file from a sam over a reference sequence

Converts sam to bed

Converts sam or bam to wig

Returns a sample from a VCF file with a specified number of results

Generate count matrix from single-cell sequencing data

Returns values sampled from the probability distribution of the mean selection coefficient for a given set of bed regions

Performs maximum likelihood estimation of selection on variants from an input VCF format file

Simulates evolution from the root of a newick tree to the extant species of the trees and then uses the leaf nodes to reconstruct the ancestral nodes and compares the answers for percent accuracy.

Returns a file of random bed regions of an input bed file

Simulates Vcf data, partitioned by divergence-based ascertainment

Simulate sequence evolution on an input fasta from the root of a newick tree to the leaf nodes

Predict amplicon products generated from PCR

Simulate alignments to a reference sequence

Contains functions for simulating VCF data

Simulate a multiallelic, haplotic Wright-Fisher population (discrete, non-overlapping generations)

Used to check for completion of SLURM job arrays (WIP).

Topologically sorts nodes in a genome graph (.gg) file

Command line statistics calculator

Convert HiC contact maps in straw format to bedpe contact peak calls

Returns allele frequency spectrum information in a text file for graphing

Adds ancestral allele to the INFO column of entries in a VCF file

Annotate Vcf records with cDNA and protein effect predictions

Filter vcf records

Options alter VCF formatting

Provides summary statistics on an input VCF file

Use the variant data in the vcf to edit an input fasta of the reference

Annotate a vcf file by querying various databases via CellBase

Returns a filtered wig based on option parameters

Perform mathematical operations on wig format data

Takes wig file and finds peaks

Provide coverage histogram for WIG format visualization files

Converts a wig to a training, validation, and testing set for the GenomeSequenceConvNet