README

These are a couple of small, hopefully useful, tools for the AMOS system.

extractScaffold is basically a rewritten extractContig, made to extract a scaffold 
instead of just a contig to a new AMOS bank. This new AMOS bank can then be used 
for analysis with amosvalidate, and visual inspection in Hawkeye.  
Bacterial sized assemblies are often small enough that one can load the 
entire assembly into Hawkeye, but in my experience it's impossible with larger 
genomes (like vertebrates) to load everything into Hawkeye, so the option of loading
just one scaffold should be useful. The scaffold view in Hawkeye might be a bit slow
however.

Usage:
extractScaffold -b <AMOS bank> -l 
- lists all scaffolds, their IID, EID, number of contigs, number of bases and span. 
Use this to find the IID of the scaffold of interest. This command for example, will 
sort the output by span size in the bank called e_coli_ca_mp_bogart.bnk:
extractScaffold -b e_coli_ca_mp_bogart.bnk -l | sort -k5,5 -n

extractScaffold -b <AMOS bank> -s <scaffold IID> -n <new AMOS bank>
- extracts the scaffold with IID together with all its reads, fragments,
libraries and contigs into a new AMOS bank. This new bank can then be inspected by
Hawkeye or validated by amosvalidate.

bank2sam is an extension of the bank2contig SAM exporting ability. It will output the 
reads in an AMOS bank as SAM entries to standard out. In contrast with bank2contig, 
the template length is included, mates are kept and you can choose between
having contigs or scaffolds as reference. (Note: In some assemblies you have negative
gaps between contigs, and if you use scaffolds as reference, you might not see a 
good alignment using the scaffold FASTA file as reference in for example Tablet. Celera
for instance will put 20 Ns between contigs with negative gaps.)
bank2sam will not output SAM headers.


Usage:
bank2sam -b <AMOS bank> -c > reads.sam
- outputs all reads in the AMOS bank to reads.sam with contigs as reference.

bank2sam -b <AMOS bank> -s 
- outputs all reads in the AMOS bank to standard out with scaffolds as reference.


Ole Kristian Tørresen