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Preprocessing

Filter low-quality, unmapped, and other short reads from next-generation sequencing data; sort short reads

Classes

BioMap Contain sequence, quality, alignment, and mapping data
BioReadQualityStatistics Quality statistics from a short-read sequence file
GFFAnnotation Represent General Feature Format (GFF) annotations
GTFAnnotation Represent Gene Transfer Format (GTF) annotations

Functions

seqfilter Filter out sequences based on specified criterion
seqtrim Trim sequences based on specified criterion
seqsplit Split sequences into separate files based on barcodes
seqsplitpe Split merged paired-end sequences into separate files

Topics

Manage Short-Read Sequence Data in Objects

Use objects to store, manipulate, and retrieve short-read sequence data

Store and Manage Feature Annotations in Objects

Use feature annotation objects to investigate and filter sequence data

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