This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes.  The package
also contains legacy support for early single-end, ungapped
alignment formats.

FASTQ input and manipulation

package-ubuntu-20.04-r-4.0.5#cran#ShortRead-1.48.0

These functions were introduced but are now deprecated or defunct.

<ul>
<li>
<code>srapply</code>. Use the BiocParallel package instead.

</li>
<li>
<code>readAligned,BamFile-method</code>. Use the GenomicAlignments
package instead.

</li>
<li>
<code>basePath()</code>

</li>
</ul>

package-ubuntu-20.04-r-4.0.5#cran#ShortRead-1.48.0#docs#deprecated

deprecated

Description

Details

ShortRead

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