guacamole

package guacamole

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Value Members

object Main extends Logging

Guacamole main class.
package alignment
package assembly
package commands

Commands (such as variant callers) that can be invoked on the command line.
package distributed
package filters

Strategies for filtering reads, filtering bases within reads, and filtering the results of variant calling (called genotypes).
package jointcaller
package kryo
package likelihood

Implementations of likelihood models.
package loci
package logging
package pileup

Answer questions like: given some reads that overlap a locus of interest, what bases were sequenced at that locus?
package reads

Classes for representing sequenced reads, mapped or unmapped.
package readsets

This package contains functionality related to processing multiple "sets of reads" (e.
package reference
package strings
package util
package variants

Classes to represent the results of variant calling.
package windowing

Step through loci in the genome and at each step consider all the reads (or any object that implements the trait ReferenceRegion) that overlap the locus.

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