i have a fasta file with 113 contigs and a reference sequence in fasta file. i have to align my contigs to the reference sequence and i have to see in which order my contigs are aligned to the reference sequence. pls can you help me which software i can use for this ?
You have to make up your mind: you can either use global-local alignment or local alignments. If you are quite sure, the contigs are not misassembled, you can use global-local alignment. You have only few contigs, therefore you can possibly use glsearch or if that doesn't work MUMer. On the other hand you won't necessarily find misassembled contigs that way, e.g. a contig that alignes only partially in two or more sections, and without testing for such contigs, you cannot know if your assembly is good. Therefore, use also local alignment tools, e.g. FASTA or BLAST.