I have got about 189 contigs from velvet by assembling 75 bp pair end sequence. Now, i get some 3k mate pair sequence, and align with the contigs. I'd like to know if there is some software can help to export scaffold or link information between the contigs.
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I have used SSPACE with nice results (Boetzer et al. 2010). You could also look at Bambus but it is a little bit more complicated to set up. -
thanks Andreas for using my software package. You can indeed scaffold your Velvet contigs with SSPACE. For best results, use both pair-end and mate pair sequences.
Have a look at this thread anyone1985;
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM
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