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Forum: Bioinformatics 04-14-2020, 12:03 AM
Replies: 1
Views: 457
Posted By bioramg
Estimation of genome size from Nanopore using jellyfish

Hi,
I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew...
Forum: Bioinformatics 04-13-2020, 11:57 PM
Replies: 2
Views: 2,651
Posted By bioramg
Estimation of genome size from Nanopore sequence using jellyfish

Hi,
I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew...
Forum: Bioinformatics 03-05-2020, 08:27 PM
Replies: 0
Views: 681
Posted By bioramg
Genome size estimation - Reg.

hi,
I would like to estimate plant mitochondrial genome size using Illumina pair-end (each one is 8 GB Raw Reads)
I used the following command for estimation:
...
Forum: Bioinformatics 03-05-2020, 05:54 PM
Replies: 6
Views: 1,376
Posted By bioramg
Thank you so much. by the way, I have used...

Thank you so much.

by the way, I have used this command to estimate genome size using the following command:
java -ea -Xmx188g -Xms188g -cp /home/pmslab/Desktop/Raman/bin/bin/bbmap/current/...
Forum: Bioinformatics 03-04-2020, 11:26 PM
Replies: 6
Views: 1,376
Posted By bioramg
Could you please give me with some examples. I am...

Could you please give me with some examples. I am new to bioinformatics. How to set desired reads...
Forum: Illumina/Solexa 03-01-2020, 10:53 PM
Replies: 0
Views: 1,048
Posted By bioramg
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 plant mitochondrial genome assembly.
Before carried out, I used...
Forum: Bioinformatics 03-01-2020, 10:15 PM
Replies: 6
Views: 1,376
Posted By bioramg
Thank you so much for your kind reply. Its...

Thank you so much for your kind reply.

Its whole genomic data that includes, chloroplast, mitochondrial and nuclear genome data. How can I choose 3/4 read? Could you please suggest.

Thank you...
Forum: Bioinformatics 02-08-2020, 04:45 PM
Replies: 6
Views: 1,376
Posted By bioramg
SPAdes assembler

Hello,
I tried to assemble a mitochondrial genome assembly with SPAdes assembler using pair-end Illumina and Nanopore sequencing data. The size of the Illumina data is 18 GB and when I do hybrid...
Forum: Bioinformatics 08-23-2018, 08:35 PM
Replies: 0
Views: 1,784
Posted By bioramg
Wink How to set cutoff coverage and expected coverage

Hi all,
I am new to mitochondrial genome assembly using whole genome sequencing. I tried to assemble with velvet with different k-mers, expected coverage - auto and coverage cutoff as auto. But I...
Forum: Bioinformatics 04-07-2014, 10:58 PM
Replies: 1
Views: 896
Posted By bioramg
Post Geneious software - Reg.

Dear friends,

Please help me. I am basically biotechnologist. I am new to handle bioinformatic tools. I would like to analyse a bacterial whole genome sequence and having geneious latest software....
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