I have the read file and assembled contigs (both in .fasta format). I need to calculate the coverage for each single contigs across the read file. I tried doing (1) indexing with bowtie (2) alignment with both with bowtie-align and tophat2. its giving me the error "Splice sequence indexing failed with err =1". Kindly help me how to proceed with the coverage calculation of each contig.
Bowtie and Tophat are short read aligners. Though tophat support longer reads like from 454 it has a limit of 1024 bases. BWA-MEM is a better option for alignment and you can get the coverage stats using samtools. I assume the 454.10species.fasta is the read file. You need to us the multi-fasta file with all the contigs to make your life easier. You can concatenate all the contig fasta files in to one and run the alignment.
What is your bowtie index name. I think you gave the read file as index and contig file as the read file. I do not understand using the option -r for your data!.