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Forum: Bioinformatics 11-02-2017, 07:30 AM
Replies: 104
Views: 41,689
Posted By Gopo
Hi Brian, I recreated the paired-end FASTQ...

Hi Brian,

I recreated the paired-end FASTQ files, performed adapter and quality trimming with bbduk, then used tadpole for error correction, and finally used tadpole in contig mode to de novo...
Forum: Bioinformatics 10-13-2017, 01:49 PM
Replies: 104
Views: 41,689
Posted By Gopo
Hi Brian, I used bbmerge and am now trying...

Hi Brian,

I used bbmerge and am now trying to error correct my paired and merged reads with tadpole at the same, but I can't seem to get the right syntax for the input

I tried the following...
Forum: Bioinformatics 10-13-2017, 11:40 AM
Replies: 104
Views: 41,689
Posted By Gopo
Hi Brian, no it did not crash- unfortunately the...

Hi Brian, no it did not crash- unfortunately the job exceeded the allowed walltime. I'll try what you suggested for Tadpole first.

@GenoMax - Thank you. Unfortunately, they were unable to finish...
Forum: Bioinformatics 10-13-2017, 10:49 AM
Replies: 104
Views: 41,689
Posted By Gopo
No I haven't, but based on the manual- I am out...

No I haven't, but based on the manual- I am out of luck as ALLPATHS-LG requires shotgun sequencing and mate pair libraries.
Forum: Bioinformatics 10-13-2017, 01:37 AM
Replies: 104
Views: 41,689
Posted By Gopo
Hi Brian, Does Tadpole have a checkpoint...

Hi Brian,

Does Tadpole have a checkpoint option, or this a possible feature to add? I ask because I am de novo assembling the axolotl genome using the available raw paired end shotgun sequencing...
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