The Staden I/O library provides a general purpose interface for reading and
writing trace files and other bioinformatics experiment files. The programmer
simply calls, for example, the read_reading function to create a "Read" C
structure with the data loaded into memory. It has been compiled and tested
on a variety of Unix systems, MacOS X and MS Windows.
srf2fasta srf2fasta extracts sequences from an SRF archive and writes them in fasta format to stdout. srf2fastq srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout. Note that Illumina also have a fastq... srf_index_hash srf_index_hash adds and index to an SRF file or replaces an existing index with a new one. In the case of concatenated SRF files only the index at the end of a... srf_info srf_info lists some simple frequency metrics on the contents of an SRF file, both in terms of how many traces there are and the sort of data held within them... srf_list srf_list lists the filenames held within one or more SRF container. To simply count the contents rather than list them specify the -c option. Note that when in...