I have assembled many chloroplast genomes and this is something we are doing on a pretty large scale now to complement other phylogenomics approaches. First, I don't think 100k reads will give you enough coverage to assemble a complete genome, but there are other good options. It is likely that you have other sequence data such as WGS reads or some kind of sequence capture data. In my experience, all sequence data sets (in plants), whether from targeted or shotgun approaches, will contain chloroplast and mitochondria fragments. You should be filtering this data anyway as it is a source of contamination, but these filtered reads can actually be combined with other data and used to assemble the chloroplast genome.
One very important step is to calculate the estimated coverage of the genome you are assembling, and you can get an estimate of the coverage by mapping to a closely related species. Picking the appropriate coverage cutoff will lead to a more complete and contiguous assembly. The most common mistake I see people making is trying to assemble with crazy high coverage (>1000X), and this does not give good results (and takes a longer to execute).
I don't think it is possible to resolve the IR regions de novo (at least, in my experience), but it can be done by using a reference.
My advice would be assemble your genome with Newbler or MIRA as Leonor suggested, then use ABACUS to order your contigs relative to the reference. That will help you fill in the gaps and transfer annotations. The caveat with this approach is that you need a reference from a closely related species because you are assuming the same order. Depending on the species being compared, this is probably a safe assumption because chloroplast genomes evolve more slowly than nuclear genomes.
100k of 454 reads is not a huge assembly, so I would try starting with a basic procedure and then see which problems arise and try to improve the assembly. I would first use the proprietary Roche assembler (aka Newbler) which you can download here, this would give you an idea of the length of contigs you can achieve:
Depending on the type of repeats (very small ones or rather large regions), the approach to deal with them will be different. Could you give us some information on the characteristics you are expecting for your repeats, so that we can help you there?
I developed a denovo assembler specially for chloroplasts and mitochondria. It can assemble a chloroplast in one contig within one hour from whole genome illumina data. I compared the results with MIRA and MITObim and it seems the quality is higher and it always assembles the whole chloroplast and only the chloroplast. As an output you get two fasta files, the only difference between them is the orientation of the region between the inverted repeats. If you blast both files against a reference you can select the correct orientation. I can send the link where you can download the tool, once it's online available.
Hi ... I have about 12GB data based on whole genome seq. by Illumina Seq.. I tried to assemble (soap denovo) 50% of the data by Genious software, but I couldn't get big contiges, the larger contig was about 70KB. so because I want to assemble complete chloroplast and mitochondria seq. this is not a proper way. do you have any idia or opinion what I have to change in my assembler (Soap denovo) to get larger contiges. Thanks