File conversion utilities
From AMOS WIKI
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
- dumpreads - report reads from bank in fasta or fastq format
- 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 SAM format
Celera Assembler Converters
To Celera Assembler
- tarchive2ca - from NCBI Trace Archive to Celera Assembler input
