Bowtie is an aligner capable of extremely fast alignments of short sequences against a much larger reference sequence.
Assembler allows easy point and click assembly of reads against a reference. It will generate reports of SNPs and other variants with Variant Calling pages. It supports Variant Calling Format (VFC) and BAM file formats. Reads can be assembled against multiple references.
Consensus and contig sequences can be exported in Fasta and Fastq formats for further analysis
If you require more details please read the Bowtie Technical help topic
Assemble reads against a reference sequence with Bowtie2.
Assemble reads against a reference sequence with Minimap2.
Viewing coverage data across a reference contig for example for RNASeq analysis