| name | bioconductor-shortread |
| description | 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, an |
| when_to_use | Use when: Iterative FASTQ Processing: Processing massive FASTQ files in memory-efficient chunks using FastqStreamer() and yield().; Random Subsampling: Drawing a random sample of reads from a FASTQ file using FastqSampler() for quick inspection.; Quality Assessment: Generating HTML quality assessment reports across multiple FASTQ files using qa() and report().; Filtering and Trimming: Removing low-quality r. Not for: For whole-genome alignments or flexible pairwise alignment, use Biostrings or pwalign instead because ShortRead is designed for basic input, QA, and filtering rather than complex alignments. |
| user-invocable | false |
ShortRead
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.70.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: BiocGenerics, BiocParallel, Biostrings, Rsamtools, GenomicAlignments
- Imports: Biobase, S4Vectors, IRanges, Seqinfo, GenomicRanges, pwalign, hwriter, lattice, latticeExtra
- Install:
BiocManager::install("ShortRead")
When to Use
- Iterative FASTQ Processing: Processing massive FASTQ files in memory-efficient chunks using
FastqStreamer() and yield().
- Random Subsampling: Drawing a random sample of reads from a FASTQ file using
FastqSampler() for quick inspection.
- Quality Assessment: Generating HTML quality assessment reports across multiple FASTQ files using
qa() and report().
- Filtering and Trimming: Removing low-quality reads or trimming tails using
nFilter() and trimTailw() before writing back to disk with writeFastq().
When NOT to Use
- For whole-genome alignments or flexible pairwise alignment, use Biostrings or pwalign instead because
ShortRead is designed for basic input, QA, and filtering rather than complex alignments.
Data Requirements
- Input: FASTQ files (e.g.,
.fastq, .fastq.gz) or legacy Solexa export files (s_N_export.txt).
- Output: Filtered FASTQ files,
ShortReadQ objects, or HTML QA reports.
- Data Structures: Reads are represented as
DNAStringSet objects and quality scores as FastqQuality or BStringSet objects.
Key Parameters
- fl: The file path to the FASTQ file being read or streamed.
- destination: The output file path used in
writeFastq().
- type: The format type specified in
qa() (e.g., type="fastq").
- dirPath: The directory path used in
readXStringColumns() to locate files.
- pattern: The regular expression pattern used to match files in
readXStringColumns().
- colClasses: A list specifying the class of each column to be read in
readXStringColumns().
Best Practices
- Use
FastqStreamer() in a repeat loop to process large FASTQ files in chunks, preventing memory exhaustion.
- Use
FastqSampler() to draw a representative subset (e.g., 1M reads) for rapid quality assessment.
- Generate a QA report using
qa() and view it in a browser using browseURL(report()) before starting downstream analysis.
- Check the quality score encoding of your FASTQ files using
encoding(quality()) to ensure accurate quality filtering.
Common Pitfalls
- Out of Memory Errors: Attempting to load an entire massive FASTQ file into memory with
readFastq(). Fix: Use FastqStreamer() to iterate through the file in manageable chunks.
- Incorrect Quality Trimming: Applying the wrong Phred score threshold because of unknown encoding. Fix: Verify the encoding using
encoding(quality(fq)) before using trimTailw().
- Slow Text Parsing: Using base R functions to read specific columns of sequence text files. Fix: Use
readXStringColumns() to quickly parse columns directly into DNAStringSet and BStringSet objects.
Alternatives
- Biostrings: For general sequence manipulation, pattern matching (
matchPDict), and whole-genome alignments.
- pwalign: For flexible pairwise sequence alignment.
Citations
- Morgan M, et al. (2009) "ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data." Bioinformatics.
References
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