Command-line alternative to Geneious assemble for Sanger sequencing data

I am doing Sanger sequencing of a construct ~2Kb using 4 primer pairs. I get back 4 .ab1 files, each with generally around 1Kb of high quality sequence and given the relatively small size of the construct these overlap significantly.

The goal is to assemble these 4 sequences into a single contig, in .fastq format (therefore retaining the per-base quality scores), and then downstream I will align this back to the reference construct using bwa mem.

I am trying to automate this procedure for hundreds of sequenced constructs. Previously this has been done manually in Geneious, using Geneious assemble (de novo assembly). The problem is, is that it is not possible to run Geneious assemble from the command line, and other tools I have used (cap3, tracy, tadpole) either fail to generate a full length contig (whereas Geneious succeeds), and / or do not output per-base quality scores (.fastq)

I would have thought that it would be a piece of cake to find an open-source tool that can match Geneious assemble, but this is not the case!

Can someone recommend a tool that I could try, or how I can optimise a tool to equal Geneious assemble?

Any suggestions appreciated!

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