I have a Burkholderia pseudomallei sequence (Miseq paired-end) and I want to perform comparative genomics against reference genomes (BPk96243, MSHR1435 and others). I already did the spades assembly but it had many nodes (700+). I can use abacas to order/align it against a reference genome but Burkholderia has 2 chromosomes which makes me confused. What should I do so that I can have Fasta files for two chromosomes (Similar to the uploaded ones)? Your help is highly appreciated. Thank you
Before using contiguate I would do a quality check of your data. For a bacteria with an expected genome size of approximately 7.0 Mbp, 700+ nodes is a lot. Did you filter out short contigs, e.g < 500 bp. If so, then you might have a contamination or your libraries have a poor quality.