metaflagstat is a tool which allows bioinformaticians and scientists alike to get an in-depth understanding of there sequencing read flag statistics. It's written in Python, free and open source, and creates pretty graphs :)
If you have any ideas or find any bugs whilst using the program - just send me an e-mail and i'll patch it in/out :)
Currently working on:
- Doing flag/read counting on a per-chromosome basis by default, allowing users to look for differences in, say, duplication rates, between chromosomes.
- The short hop from counting per-chromosome to also counting user-defined regions (from a BED file) to check mappability in regions, say, repeat regions, between samples.
- Storing insertion length distributions for different read flag combinations, and different chromosomes.
- Visa versa, storing read flags counts at different insertion length windows.
- Convert a query into samtools notation to quickly get a file of the reads you counted.
- Offline mode
All the best!
- Query parser has been remade. It now excepts all valid algebra, and understands BODMAS :]
- Chart options / CSS has been tweaked to give your data more screen space - no more tiny bars when you analyse more than 10 files at once! ;~)