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 .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

From Celera Assembler

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