AMOS Conversion Tools
Below is a listing of the main conversion tools available in AMOS.
For many of these programs we are still working on
documentation.
If there is no link from the program name to a page
containing
the relevant documentation, you can still get a good idea of how to use
the program by running it with the "-h" option.
- To AMOS formats
- Reads,
Libraries, etc.
- From
Trace Archive
- From
sequence/quality files
- From
Celera Assembler
- From
.phd files
- Contigs,
Scaffolds, etc.
- From
Assembly Archive
- From
.ACE files (phrap, arachne)
- From
Celera Assembler
- From
TIGR assembler
- From AMOS formats
- Reads,
Libraries, etc.
- To
Celera Assembler
- To
sequence/quality files, etc.
- Contigs,
Scaffolds, etc.
- To
Assembly Archive
- To .ACE
files
- To TIGR
Assembler
- To FASTA
- Celera Assembler
Converters
- To Celera
Assembler
- From Celera
Assembler
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
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