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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,... -
SPAdes update
I cannot remember how I did this the last time I updated. Trying to update to spades 3.14.1. Spades is set to /usr/local/bin/spades.py. I think it was... -
Spades: Failed to determine erroneous kmer threshold. Threshold set to: 22
Hi,
Thank you for developing SPAdes for hybrid assembly.
I tried to assemble Illumina pair-end with Oxford Nanopore Sequence for... -
SPADES: Failed to determine erroneous kmer threshold. Threshold set to: 22
Hi,
Thank you for developing SPAdes for hybrid assembly.
I tried to assemble Illumina pair-end with Oxford Nanopore Sequence for... -
SPAdes duplicate contigs between chromosome and plasmid
Hi all,
Has anyone had any issues with SPAdes outputting duplicate sequences between plasmid and chromosome assembly outputs? I have an... -
Retrieve read IDs from SPAdes contigs
Hi everyone,
I'm using SPAdes 3.12 to assemble contigs using reads. The question is, is there any way to retrieve the reads used to assemble the... -
Assembly with trimmed FASTQ files fail
Hello,
spades is working fine when I am using untrimmed fastq files.
I am using Trimmomatic to trim reads (SLIDINGWINDOW:30:20)... -
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... -
how do i reduce misassemblies in spades?
I'm new to spades and i've started on some genomes which i previously assembled in velvet (~6 Mb chromosome plus one ~40 Kb plasmid, and a few long repeats... -
Independent assemblies from NextSeq FASTQs
Haven't found a thread answering this question yet, apologies if it already exists somewhere.
I'm assembling some very large metagenomes... -
Multiple libraries of different lengths - single or seperate assemblies?
Hi!
I have three Ion torrent libraries; a 600bp, 400bp and a 200bp library. I intend to use SPAdes to assemble the reads into contigs but... -
Please help with assembly 2x250 bp with 350 insert
Hi folks,
I have got data generated from 2x250 bp with 350 bp insert for fungal genome assembly. I got very good results from SPAdes,... -
SPAdes 3.9.0 on MacOS Sierra (10.12.1)
I've tried installing SPades 3.9.0 on MacOS Sierra from the binaries, from source, and using conda. Running spades.py --test gives me the same error... -
Minimum contig coverage to keep
Dear all,
I am working on de novo assembly of bacterial genomes. Genomes were sequenced with Miseq 2x250 libs with an average coverage... -
SPAdes plasmids output
Hello all. I have done a plasmidSPAdes run on my bacterial reads to look for any plasmids. In the final output directory, I have the contigs.fasta file...Last edited by ronaldrcutler; 07-26-2016, 07:51 PM.
