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haowenz / chromap

Fast alignment and preprocessing of chromatin profiles
https://haowenz.github.io/chromap/
MIT License
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Use Cases for Chromap compared to BWA-MEM #109

Open sqhang opened 2 years ago

sqhang commented 2 years ago

Thanks for your great work in developing Chromap, an ultrafast aligner for chromatin profile alignment!

In the paper, you mentioned that Chromap is much faster than popular aligners such as BWA-mem and Bowtie, and Chromap is comparable with those aligners in alignment accuracy. Yet, I wonder what are the analysis/features that Chromap does not have while BWA-mem and Bowtie do. In other words, are there any use cases that you would not recommend to use Chromap in lieu of BWA-mem and Bowtie. One example might be SNP calling. If we want to conduct downstream analysis of SNP calling on the aligned data, will Chromap help produce alignments down to single-base pair resolution (not just the coordinates, but the match/mismatch for each aligned genomic position)?

Let me what you think. Thanks!

haowenz commented 2 years ago

Chromap can generate alignment in SAM format, which has the base-level alignment (in CIGAR). But in our paper, we didn't test SNP calling but focus on other applications in chromatin biology which only need the mapping positions or intervals. You are welcome to test Chromap in the way you want and we are happy to learn from your results to improve Chromap if necessary.