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Dear Bob,
We have a puzzling case with lastz version 1.04.15 that raises 2 questions.
We are aligning human exons against larger genomic chunks from other organisms with very sensitive paramet…
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To whom it may concern,
My name is Yunzhe Jiang, a senior undergraduate majoring in Bioinformatics at Shanghai Jiao Tong University. I am using the LASTZ program to do the alignments for my undergr…
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Hi,
I have several bacteria genomes. There are several sequences in a single genome. Genome size is small, like 3M.
My aim is to get a multiple genome alignment. When using lastz to do pairwise alig…
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Hello,
I don't know if you are accepting suggestions for improvements, but I was wondering if you were perhaps open to implementing [geometric hashing](https://www.biorxiv.org/content/10.1101/2020.…
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Is there a way to output unaligned sequences in LASTZ? I am trying to generate some summary metrics and it would be great if I can just count unaligned sequences from the output.
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Hi Dr. @MichaelHiller
I have couple of queries regarding my TOGA outputs. I am working with vertebrates genomes (size ranging from 550Mb to 1Gb, all genomes that I considered are of very good qual…
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Hi,
We are performing genome alignments using Progressive Cactus software and toil on Amazon Web Services. We don't have much computational background, and are getting the following error (several ti…
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when I run LASTZ_SV_pipeline, the results in SVnew is empty
the screen says:
Use of uninitialized value in addition (+) at ../src/SVcallerl1.pl line 46, chunk 1.
Use of uninitialized value in …
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I would like to know how each input file was obtained, and whether I can also use hg38 as a reference genome to apply to other projects.
My current understanding is that the two 2bit files are conver…
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Good day,
I'm currently working on the assembly of a large mammalian genome. I would like to perform the reference-assisted scaffolding using ragout. However, I cannot run progressive cactus on the g…