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Data Import and Management

Import next-generation sequencing data and feature annotations from SAM, BAM, FASTA, FASTQ, SOAP, GTF, GFF, and Bowtie files; manage large data sets containing millions of single- and paired-end short reads


fastainfo Return information about FASTA file
fastaread Read data from FASTA file
fastawrite Write to file using FASTA format
fastqinfo Return information about FASTQ file
fastqread Read data from FASTQ file
fastqwrite Write to file using FASTQ format
saminfo Return information about Sequence Alignment/Map (SAM) file
samread Read data from Sequence Alignment/Map (SAM) file
baminfo Return information about Binary Sequence Alignment/Map (BAM) file
bamread Read data from Binary Sequence Alignment/Map (BAM) file
bamindexread Read Binary Sequence Alignment/Map Index (BAI) file
goannotread Read annotations from Gene Ontology annotated file
soapread Read data from Short Oligonucleotide Analysis Package (SOAP) file


BioIndexedFile Allow quick and efficient access to large text file with nonuniform-size entries
BioMap Contain sequence, quality, alignment, and mapping data
BioRead Contain sequence and quality data
BioReadQualityStatistics Quality statistics from a short-read sequence file
GFFAnnotation Represent General Feature Format (GFF) annotations
GTFAnnotation Represent Gene Transfer Format (GTF) annotations

Examples and How To

Work with Large Multi-Entry Text Files

Example of using a BioIndexedFile object to extract data from a large multi-entry text file

Manage Short-Read Sequence Data in Objects

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


Data Formats and Databases

The Bioinformatics Toolbox™ accesses many of the databases on the Web and other online data sources.

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