Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • idba_ud coassemble Miseq 2x250 and HiSeq 2x100 reads?

    Hi folks,

    I'm curious if anyone else has tried to use idba_ud co-assemble longer MiSeq data (2x250) with HiSeq data (2x100)? I've tweaked the source code to accept longer reads from MiSeq and also to increase the allowable maxK up to 250 (which uses lots of memory but increases N50 considerably on my data). I'm catted together interleaved fasta files from my MiSeq and HiSeq runs and am currently running a coassembly on our big memory machine like so:

    ~/software/idba-1.1.0_hack2/idba-1.1.0/bin/idba_ud -r miseq.hiseq.QC.i.fasta -o hyb.1 --num_threads 8 --min_contig 500 --maxk 250

    It recognized the input read length as 100bp - though it should range from shorter than that to 250bp (due to quality trimming, reads are variable length). Will this affect how the algorithm treats variable length reads? Any obvious problems anticipated?

    Cheers,
    Lizzy

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X