View source for File conversion utilities

== Overview ==

The ASM File converters are a collection of utilities for converting sequence and assembly data between the most widely used data formats as well as to and from the AMOS message format. Examples of the data handled by these utilities are: Trace Archive data and ancillary information, .ACE assembly format, TIGR Assembler input and output formats, Celera Assembler message format, and Arachne input and output formats.




== To AMOS formats ==

=== Reads, Libraries, etc. ===
==== From Trace Archive ====

* [[tarchive2amos]] - from NCBI Trace Archive and/or Assembly archive to AMOS. Also simple .seq/.qual to amos converter


==== From sequence/quality files ====

* [[tarchive2amos]] - from NCBI Trace Archive and/or Assembly archive to AMOS. Also simple .seq/.qual to amos converter
* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS


==== From Celera Assembler ====

* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS


==== From .phd files ====

* [[phd2afg]] - from .PHD files to AMOS message file.


=== Contigs, Scaffolds, etc. ===
==== From Assembly Archive ====

* [[tarchive2amos]] - from NCBI Trace Archive and/or Assembly archive to AMOS. Also simple .seq/.qual to amos converter


==== From .ACE files (phrap, arachne) ====

* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS


==== From Celera Assembler ====

* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS


==== From TIGR assembler ====

* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS



== From AMOS formats ==
=== Reads, Libraries, etc. ===
==== To Celera Assembler ====

* [[amos2frg]] - from AMOS message file to Celera Assembler message file


==== To sequence/quality files, etc. ====

* [[amos2sq]] - from AMOS message file to .seq/.qual files
* [[amos2mates]] - from AMOS message file to Bambus .mates file
* [[select-reads]] - utility to select reads by iid/eid from a bank. Allows both inclusive and exclusive queries.

=== Contigs, Scaffolds, etc. ===
==== To Assembly Archive ====

====To .ACE files====

* [[amos2ace]] - the name says it all - from AMOS to .ACE format

==== To TIGR Assembler ====

* [[bank2contig]] - from AMOS bank to TIGR Assembler .contig files (similar to GDE .align files).

==== To FASTA ====

* [[bank2fasta]] - from contigs stored in a bank to multi-fasta file of their consensus.
* [[bank2scaff]] - from scaffolds stored in a bank to a variety of formats, including multi-fasta file

==== To SAM ====

* [[bank2contig]] - from contigs stored in a bank to the [http://samtools.sf.net SAM] format


== Celera Assembler Converters ==
=== To Celera Assembler ===

* [[tarchive2ca]] - from NCBI Trace Archive to Celera Assembler input

=== From Celera Assembler ===

* [[toAmos]] - universal converter from many sequence/assembly formats to AMOS
* [[ca2ace]] - from the output of Celera Assembler to .ACE files