# WGS Alignments that tolerate large, unknown, non-genomic insertions

**URL:** <https://help.galaxyproject.org/t/wgs-alignments-that-tolerate-large-unknown-non-genomic-insertions/6517>\
**Category:** usegalaxy.org support\
**Tags:** workflow\
**Created:** [August 16, 2021, 7:09pm UTC](https://help.galaxyproject.org/t/wgs-alignments-that-tolerate-large-unknown-non-genomic-insertions/6517 "2021-08-16T19:09:43Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Dhruv\_Patel](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dhruv_patel/32/2206_2.png) [@Dhruv\_Patel](https://help.galaxyproject.org/u/Dhruv_Patel)\
**Post date:** [August 16, 2021, 7:09pm UTC](https://help.galaxyproject.org/t/wgs-alignments-that-tolerate-large-unknown-non-genomic-insertions/6517/1 "2021-08-16T19:09:44Z")

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I completed a WGS alignment using 150PE fastq reads via BowTie2 to a locally installed plant genome. The alignment worked well, and I am able to visualize the reads by Integrated Genome Viewer (IGV). However at my site of interest, I see that I have a large set of paired reads where the pair is not mapped. I am thinking that I have a non-reference sequence insertion at that site that is not tolerated by BowTie2 and is discarded during sequence processing, and there doesn’t seem to be an intuitive way to find my discarded reads of interest.

Is anyone aware of workflows on Galaxy that may tolerate non-genomic sequences better? Maybe de novo genome assembly workflows that can handle large genomes (400Mbp)? Apologies in advance if this is not a Galaxy question, but is instead one for a more bioinformatically-oriented forum.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [August 16, 2021, 11:40pm UTC](https://help.galaxyproject.org/t/wgs-alignments-that-tolerate-large-unknown-non-genomic-insertions/6517/2 "2021-08-16T23:40:09Z")

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Hi @Dhruv_Patel

Reads that do not align with the reference can be output by the tool. See the option “Write unaligned reads (in fastq format) to separate file(s)” on the `Bowtie2` tool form (near the top).

And you could certainly try assembly options to reconstruct any novel regions. Tutorials:

> **[Galaxy Training](https://training.galaxyproject.org/training-material/)**
>
> Collection of tutorials developed and maintained by the w...

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 17, 2026, 6:58am UTC](https://help.galaxyproject.org/t/wgs-alignments-that-tolerate-large-unknown-non-genomic-insertions/6517/3 "2026-03-17T06:58:42Z")

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Closed on March 17, 2026, 6:58am UTC