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...
19 results in 0.0031 seconds.
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Retrieve read IDs from SPAdes contigs
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reads align but contigs do not??
Here is something that puzzles me:
I have 4000 reads that align to my reference genome. I can visualize them, they cover maybe 80 % or a little... -
Getting coverage of each contig from velvet output
Is there a way to get the coverage on each contig from velvet? The Log file gives the median coverage only and I can't really understand the meaning of... -
Problem replacing contigs in a dbsnp vcf using Picard SortVcf
Right now I'm trying to change the contigs in the dbsnp vcf to match those of my reference genome (from 1, 2, ..., Y, MT to chrM, chr1, chr2,...)
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Remove subset of good reads to improve genome assembly
Hello seqanswers,
I'm de novo assembling a diploid genome (haploid genome = 200Mb) with reads from Illumina Hiseq V4 2x125 (high-output)... -
Code for identifying and renaming contigs
Just completed an assembly and was wondering if there is any code around which will take my assembly, blast it, get the best hits and rename the contigs... -
Identifying unique alleles/haplotypes for contigs
Dear All,
I have successfully created contigs using paired-end RAD data, and equally successfully mapped raw reads from different species... -
blastall blastx filter different hits on one contig
Dear all,
I performed a blastx of some thousand contigs of size between 1500 and 5000 bp against uniref-protein database. To speed it up... -
Is this a valid GFF3 file for HTSeq?
Hi there,
I created a gff3 file from GenBank file containing multiple contigs (using Bioperl 'genbank2gff3.pl' tool) . In order to run HTSeq... -
NCBI standards for genome annotation after contig reduction
Hi community,
I have been using a bacterial draft genome from GenBank for RNA-seq project. In order to reduce genome contig number, I used... -
Contig Integrator for Sequence Assembly (CISA) error
Hi,
I am trying CISA program to integrate a set of contigs obtained with different assemblers and it seems pretty easy to run. Just 2... -
contig mapping reference blat psl result handle
I mapped my resequencing contigs to the reference which is the same species with blat to locate these contigs, than I want to join the ordered contigs... -
Quality of Assembly based on Ion Torrent Data (microbial genome)
Hi All !
After some good exercise with data, I obtained following results as follows: Ion-Torrent Data for a 5 Mbp microbial genome: Acquired... -
Does anyone do contig analysis in Java?
Does anyone do contig analysis (code coverage, SNP/ variation detection, assembly error detection etc) using software written in Java? Software libraries... -
truncation of contig in velvet
Hi I have playing with velvet and I found this strange artifact when assembling data. When I have the following 2 sequences they get assembled into 2...
