We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very good reference genome. We have been mapping our lcg one at a time to the reference genome using bwa and Bowtie2 then using samtools and GATK to explore SNPs/Indels etc.
Is it possible to map all of our lcgs to the reference genome in a single run?
We would like to do various sliding window analyses along our reference genome with all lcgs mapped as a single alignment.
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...