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staden-io-lib-utils

programs for maniuplating DNA sequencing files

Variants:
The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

This package contains the programs that are distributed with the Staden io_lib for manipulating and converting sequencing data files, and in particular files to maniuplate short reads generated by second and third generation sequencers and stored in SRF format.

Homepage:
Package version:1.12.4-1
Architecture:amd64
Distribution:Debian
Filename:staden-io-lib-utils_1.12.4-1_amd64.deb

/usr/share/doc/staden-io-lib-utils/README.gz

			IO_LIB VERSION 1.12.4
			=====================

Io_lib is a library of file reading and writing code to provide a general
purpose trace file (and Experiment File) reading interface. The programmer
simply calls the (eg) read_reading 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.

The directori
more»

/usr/share/man/man1/srf2fasta.1.gz

srf2fasta(1)                Staden io_lib               srf2fasta(1)



NAME
       srf2fasta - Converts SRF files to fasta format


SYNOPSIS
       srf2fasta  [-C] srf_archive


DESCRIPTION
       srf2fasta  extracts  sequences from an SRF archive and writes
       them in fasta format to stdout.


OPTIONS
       -C     Masks out sequences tagged as bad quality.


EXAMPLES
       To extract only 
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/usr/share/man/man1/srf2fastq.1.gz

srf2fastq(1)                Staden io_lib               srf2fastq(1)



NAME
       srf2fastq - Converts SRF files to Sanger fastq format


SYNOPSIS
       srf2fastq  [options] srf_archive ...


DESCRIPTION
       srf2fastq  extracts  sequences and qualities from one or more
       SRF archives and writes them in Sanger fastq format  to  std‐
       out.

       Note that Illumina also have a fa
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/usr/share/man/man1/srf_index_hash.1.gz

srf_index_hash(1)           Staden io_lib          srf_index_hash(1)



NAME
       srf_index_hash -
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/usr/share/man/man1/srf_info.1.gz

srf_info(1)                 Staden io_lib                srf_info(1)



NAME
       srf_info  -  Lis
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/usr/share/man/man1/srf_list.1.gz

srf_list(1)                 Staden io_lib                srf_list(1)



NAME
       srf_list - Lists
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/usr/share/doc/staden-io-lib-utils/changelog.Debian.gz

staden-io-lib (1.12.4-1) unstable; urgency=low

  * New upstream release, with changes on endianness
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/usr/share/doc/staden-io-lib-utils/changelog.gz

===============================================================================
2010-07-06: RELEASE 
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