Hi,

Recently, I have assembled large tree genome and received multiple contigs. Dotplot analysis using alignments from minimap2 showed that some of the those contigs could merged to form a scaffold (when aligned to the reference). Furthermore, I have stat analysis using samtools and now can view the alignment in NCBI genome viewer (.BAM and.BAI).

Is there any good tool available to view those alignment and simultaneously provide:

1. Merge assembled contigs automatically at overlap coordinates
2. can provide info about consensus sequences
3. can discard contigs which does not match

Thank you