User: benv

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benv710
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710
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Location:
Canada
Last seen:
1 year, 11 months ago
Joined:
5 years, 10 months ago
Email:
b***@bcgsc.ca

Posts by benv

<prev • 79 results • page 1 of 8 • next >
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Answer: A: Make error for abyss-PE with many libraries
... Hi @ck178807, Your `abyss-pe` command looks good in principle. Your problem has something to do with the newlines and line continuations ("\" characters) in your command. I sometimes struggle with this myself. Please try collapsing your command line into a single line, confirm that it fixes the ...
written 2.2 years ago by benv710
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Comment: C: ABySS min = 500 ; how to change it
... That is exactly right, @h.mon. The 500 bp length threshold is only used by `abyss-fac` when calculating contiguity stats (e.g. N50). (`abyss-fac` has a `-t` option for changing the threshold, which defaults to 500 bp.) The output assembly FASTA files from ABySS are never filtered by sequence lengt ...
written 2.2 years ago by benv710
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Answer: A: How does the memory requirements of abyss scale ?
... @lieven.sterck, You have the right idea with respect to distinct k-mers -- the memory usage of ABySS is linear w.r.t. the number of distinct k-mers in the input reads. The number of distinct k-mers in the data set depends jointly on: (i) genome size, (ii) sequencing error rate (sequencing errors c ...
written 2.8 years ago by benv710
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Answer: A: Is the Abyss contig and scaffold phased?
... Hi James, No, ABySS does not attempt to create a phased assembly. Like most de novo genome assemblers, it is a haploid assembler (it collapses heterozygous regions into a consensus). W.r.t. to your contig alignments in IGV, it is normal to see pileups in repeat regions, but you generally should no ...
written 2.9 years ago by benv710
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Comment: C: unrecognized error in the abyss assembly software
... I'm not a Conda user, but it appears that you have a version mismatch between the installed versions of ABySS and gcc (libgomp is a part of gcc that implements multithreading.) In other words, ABySS was compiled with some other version of gcc (libgomp) than what is installed in Conda. I noticed th ...
written 2.9 years ago by benv710
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Comment: C: SNP calling from a scaffold.fa file
... Thanks, @pfs! I was just about to suggest the same. ...
written 3.0 years ago by benv710
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Comment: C: Reading single-end reads takes forever
... Sorry for slow response. To run a single-end assembly only, specify the input single-end reads with `se=""` or `in=""` and add the word "unitigs" to the end of the `abyss-pe` command. ...
written 3.1 years ago by benv710
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Comment: C: ABySS and Velvet "number of contigs and contig length in pair-end and single-en
... I am not familiar with Velvet usage, but if you provide the `abyss-pe` command and verbose log output (add "v=-v" to `abyss-pe` command), I could have a look. Output of `abyss-fac` (N50 etc.) is helpful as well. It is standard practice to run assemblies for a range of k-mer sizes to achieve the be ...
written 3.1 years ago by benv710
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Comment: C: Bosst configure error
... It is really hard to tell what is wrong from the `configure` output alone. If you look for the Boost checks in the `config.log` file it will give you more info about why the checks failed. If you like, you can post your config.log (post here, send e-mail to benv at bcgsc dot ca, or post to GitHub ...
written 3.2 years ago by benv710
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Comment: C: Rescaffolding a genome assembly?
... Good to know. Thanks for posting back! ...
written 3.2 years ago by benv710

Latest awards to benv

Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 2.8 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3.2 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3.2 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3.3 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Reading single-end reads takes forever
Scholar 3.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
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Scholar 3.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 3.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 3.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
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Scholar 5.0 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 5.0 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
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Scholar 5.6 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS

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