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Background  Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions.    Results  To facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose  SAUTE  and  SAUTE_PROT  assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for  SAUTE  and  SAUTE_PROT , respectively.    Conclusions  For RNA-seq, comparisons with  Trinity ,  rnaSPAdes ,  SPAligner , and  SPAdes  assembly of reads aligned to target proteins by  DIAMOND  show that  SAUTE_PROT  finds more coding sequences that translate to benchmark proteins. Using  AMRFinderPlus  calls, we find  SAUTE  has higher sensitivity and precision than  SPAdes ,  plasmidSPAdes ,  SPAligner , and  SPAdes  assembly of reads aligned to target regions by  HISAT2 . It also has better sensitivity than  SKESA  but worse precision.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12859-021-04174-9.

SAUTE: sequence assembly using target enrichment