36 results in 0.0027 seconds.
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Resources to learn genome assembly workflow for small genomes (like viruses)
I have sequencing data of a few samples of a `DNA genome virus`. I'd like to learn `de novo assembly` of the `short reads`, making scaffolds from it,... -
Contig and scaffold N50
Hi all,
Is it possible for contig and scaffold N50s to be very similar (e.g. within 2-3k bp) or the exact same? I have seen a few examples... -
Re-mapping contigs or predicted genes?
Hi!
I'm quite new to bioinformatics and am currently running into a dilemma on how to approach my re-mapping.
I have successfully assembled... -
Low K-mer coverage from a SPAdes assembly
Hi everyone!
I kind of asked the question on my presentation thread, but I think this is a better place to make sure I reach people who... -
raw illumina reads or assembled contigs for Taxonomy
Hello!
I am having whole genome sequenced metagenomic data that is assembled using meta-velevt. I want to check taxonomic classification... -
Align full length contigs instead of reads
Hello,
Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available.... -
CAP3 - strange behaviour, never finishes running (2xXeon 2620v4/Ubuntu 16.04.2 LTS)
I am running CAP3 under Ubuntu 16.04.2 LTS (2xXeon 2620v4) to assemble a very small data set (31 contigs in 7k-700k bp range). I am doing that to check... -
can't export complete coverage image from Tablet
Hi everyone
I'm using Tablet to visualize contigs built from velvet but in one case i have a big coverage image that i can't export complete... -
Extracting Unmapped Contigs
Hello,
I've assembled some contigs from a sequenced strain and aligned them back to the reference with Mauve. I'm interested in studying... -
de novo contigs don't match mapped reads
Hi all,
I'm confused about the results I get when I map the reads back to the contigs from Abyss. There are a number of contigs where the... -
Evaluating RAST annotation
Hi everyone,
I'm doing an annotation using RAST in a non-ordered contigs genome and I'm having trouble to determine if the annotation was done... -
determining number of reads in a contig using clc genomics work bench
Is it to possible to calculate the number of reads in a contig or number of reads mapping back to a contig using CLC genomics workbench? How? -
Basic question mapping read/contigs (Bowtie2)
Hi,
I am learning bioinformatics and have a basic question about bowtie2.
I got 2 different sets of single-end sequencing reads:... -
Assembled contigs vs short reads
I have recently finished assembling some metagenome sequences and after assigning function to my contigs I see that most genes belong to three specific... -
To remove or to keep duplicates in alignment of NGS paired reads to a set of contigs
I have a SAM file containing alignments of NGS paired reads against a set of assembled contigs (de novo).
If I might need to infer some...
