# How to set min\_alignment\_len

**URL:** <https://forum.biobakery.org/t/how-to-set-min-alignment-len/1715>\
**Category:** MetaPhlAn\
**Created:** [February 23, 2021, 2:48am UTC](https://forum.biobakery.org/t/how-to-set-min-alignment-len/1715 "2021-02-23T02:48:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![junghun](https://avatars.discourse-cdn.com/v4/letter/j/71e660/32.png) [@junghun](https://forum.biobakery.org/u/junghun)\
**Post date:** [February 23, 2021, 2:48am UTC](https://forum.biobakery.org/t/how-to-set-min-alignment-len/1715/1 "2021-02-23T02:48:00Z")

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Hello everyone!

I am trying to have taxonomical data from SRR1778456, and I got some questions. First sorry if it is very obvious question, and thank you for your kindness. The SRR1778456 has read length of 90. so if I use --bt-ps -very-sensitive-local option and min\_alignment\_len 100 as default, it gets nothing as result. So I’ve been trying to set min\_alignment\_len under 90 and tried 70, 60, 50 and got all different results. Is there any guidelines to set min\_alignment\_len ? or do you have any suggestions?

Thanks again!

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [March 4, 2021, 8:20am UTC](https://forum.biobakery.org/t/how-to-set-min-alignment-len/1715/2 "2021-03-04T08:20:25Z")

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`SRR1778456` is a short-read metagenome, I’d advise you to run MetaPhlAn using the default end-to-end preset. The local alignment option is advisable to use when you have reads longer than 150 bp.