# \#bwa\_mem2 **URL:** https://help.galaxyproject.org/tag/bwa-mem2/429.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [BWA-MEM2 input file naming](https://help.galaxyproject.org/t/bwa-mem2-input-file-naming/17452)
**Author:** [@pbay653](https://help.galaxyproject.org/u/pbay653)\ **Replies:** 2\ **Last updated:** [February 13, 2026, 1:37am UTC](https://help.galaxyproject.org/t/bwa-mem2-input-file-naming/17452 "2026-02-13T01:37:40Z")
Firstly in order to get this to work I had to rename both fastqsanger files to exactly the same name, either R1/R2 or 1/2 or F/R did not work, after that it seems to work but I have other problems if someone can read the… --- ## [Error in BWA-mem2 alignment](https://help.galaxyproject.org/t/error-in-bwa-mem2-alignment/17321)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 7\ **Last updated:** [January 19, 2026, 3:06pm UTC](https://help.galaxyproject.org/t/error-in-bwa-mem2-alignment/17321 "2026-01-19T15:06:43Z")
I have used BWA-mem2 for sample alignment with reference human pappiloma virus. The reference is not available on the Galaxy Europe platform, hence I uploaded the reference. After successful alignment, when selecting th… --- ## [BWA MEM2 tool troubleshooting](https://help.galaxyproject.org/t/bwa-mem2-tool-troubleshooting/16358)
**Author:** [@huiping](https://help.galaxyproject.org/u/huiping)\ **Replies:** 5\ **Last updated:** [October 8, 2025, 7:38pm UTC](https://help.galaxyproject.org/t/bwa-mem2-tool-troubleshooting/16358 "2025-10-08T19:38:38Z")
Dear Sir or Madam, When using your BWA-MEM2 tool to align sequencing reads to a reference genome, I noticed apparent frameshift mutations in a few reads — not soft-clippings (see example below). These changes seem to re… --- ## [BWA-MEM2 built-in drop down menu](https://help.galaxyproject.org/t/bwa-mem2-built-in-drop-down-menu/12276)
**Author:** [@lauracristinahdz](https://help.galaxyproject.org/u/lauracristinahdz)\ **Replies:** 1\ **Last updated:** [April 23, 2024, 1:58pm UTC](https://help.galaxyproject.org/t/bwa-mem2-built-in-drop-down-menu/12276 "2024-04-23T13:58:25Z")
Hi! I was trying to use BWA-MEM2, but the built-in drop down menu is not displayed. In contrast, the drop down menu is correctly displayed in BWA-MEM. Can this be fixed? --- ## [Extract rDNA reads from sequencing reads](https://help.galaxyproject.org/t/extract-rdna-reads-from-sequencing-reads/12052)
**Author:** [@Isa](https://help.galaxyproject.org/u/Isa)\ **Replies:** 3\ **Last updated:** [April 9, 2024, 7:28pm UTC](https://help.galaxyproject.org/t/extract-rdna-reads-from-sequencing-reads/12052 "2024-04-09T19:28:00Z")
Hello, I’m working on an internship project involving galaxy, where I need to focus on a specific chromosome sequence. The data I have consists of whole genome NGS reads. Initially, I attempted to map these reads agains… --- ## [Bwa-mem2 data manager???](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727)
**Author:** [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)\ **Replies:** 2\ **Last updated:** [February 18, 2024, 3:38pm UTC](https://help.galaxyproject.org/t/bwa-mem2-data-manager/11727 "2024-02-18T15:38:55Z")
Hello, Bwa-mem2 is presented in toolshed for local Galaxy install, but I cannot find it\`s data manager to build indexes. How can I start bwa-mem2 on local Galaxy? Thank you. --- ## [There are no locally cached or built-in genomes on use.galaxy.org](https://help.galaxyproject.org/t/there-are-no-locally-cached-or-built-in-genomes-on-use-galaxy-org/11232)
**Author:** [@billy.l](https://help.galaxyproject.org/u/billy.l)\ **Replies:** 1\ **Last updated:** [November 29, 2023, 12:58am UTC](https://help.galaxyproject.org/t/there-are-no-locally-cached-or-built-in-genomes-on-use-galaxy-org/11232 "2023-11-29T00:58:37Z")
I’ve been seting my galaxy workflow aside for a month. Today I came back to run a workflow, Galaxy told me that I need to choose a correct genome. I tried “locally cached” in the menu, but no genomes were listed. This ha… --- ## [Troubleshooting BWA-MEM2 resources under Docker Galaxy](https://help.galaxyproject.org/t/troubleshooting-bwa-mem2-resources-under-docker-galaxy/10819)
**Author:** [@Ann\_Holtz-Morris](https://help.galaxyproject.org/u/Ann_Holtz-Morris)\ **Replies:** 1\ **Last updated:** [September 20, 2023, 9:24pm UTC](https://help.galaxyproject.org/t/troubleshooting-bwa-mem2-resources-under-docker-galaxy/10819 "2023-09-20T21:24:12Z")
Hi Jenna, I ran into this same error. With fastp cleaned data, I can use bwa-mem2 to run a dataset to 1 or 2 genes of the reference hg38. I then tried running the 48 pairs in the collection against the single gene. Tha… --- ## [BWA-MEM2 Built in Genome Indexes is not working.](https://help.galaxyproject.org/t/bwa-mem2-built-in-genome-indexes-is-not-working/10363)
**Author:** [@RobHuffster31](https://help.galaxyproject.org/u/RobHuffster31)\ **Replies:** 1\ **Last updated:** [July 2, 2023, 2:16am UTC](https://help.galaxyproject.org/t/bwa-mem2-built-in-genome-indexes-is-not-working/10363 "2023-07-02T02:16:38Z")
The drop down for built in genome indexes is not working.