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• package-info.java

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net.maizegenetics.dna.read.package-info Maven / Gradle / Ivy

/**
 * Data structures for holding raw sequence data (only Fastq currently), including Illumina, PacBio, Nanapore, etc.
 * This package provides methods for quality control, reformatting and contiging pair end sequence.
 *

 * Definitions:
 * 
Read:  a single sequence from a sequencer
 * 
PERead a paired end sequence, including ReadF and ReadB
 * 
ReadF:  a single sequence from paired end sequence of R1
 * 
ReadB:  a single sequence from paired end sequence of R2
 * 
Pcontig:  a Pcontig is formed by a PE Tag whose forward tag and backward tag have overlap 
 *

 * This package provides methods for quality control, reformatting and contiging pair end sequence.
 * All sequences are stored in string. Large chunk of reads do not go into memory
 */
package net.maizegenetics.dna.read;