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Mark · 10-29-2020, 03:58 PM

I'm using PacBio's "variantCaller" tool (v6) to call variants on some older RSII subread data I aligned with blasr. The reference is 14845...

Mark · 10-29-2020, 12:49 PM

I'm using your "variantCaller" tool (v6) to call variants on some older RSII subread data I aligned with blasr. The reference is 14845 bp....

maxrempel · 06-10-2019, 09:54 AM

Can you recommend a DNA alignment program that can sort heterogeneous sequences into groups and produce multiple consensuses?
For example
...

phleroy · 01-25-2019, 01:02 AM

Hello

I have sequenced a BAC clone with PacBio RSII
To make the assembly I used Facon through pbbioconda and for polishing I used quiver...

SDK · 01-19-2018, 10:13 AM

Hello All,

I've got 2 distinct but related problems...well 3 problems if you count that I'm not a bioinformatician! I've just completed...

GermanoPolo · 11-24-2017, 03:03 AM

Hello guys!

I’m looking for a software that can find unknown consensus sequences between some promoters regulated from the same transcriptional...

marco12345 · 09-27-2017, 06:32 AM

Hi,

I have a phylogenetic trees built from alignments of sequences of a set of genes (1 gene per tree), where the final nodes are the individual...

AB.PATEL · 01-26-2017, 07:46 PM

HI

I have performed reference based consensus generation. Next I have mapped back reads to consensus and performed SNP calling. Surprisingly...

Neuls · 12-15-2016, 11:45 PM

Hi,

Our lab is currently sequencing a 1000pb gene fragment. They sequence foward and reverse strand, so they get the same strand sequenced...

MinnSeq · 09-21-2015, 01:22 PM

Hi everyone,

I just got my first PacBio data in and would like some advice on how to handle the data. I submitted a 1KB amplicon library...

Lilith-Elina · 04-08-2013, 01:38 AM

Hi there,

I've been using this command to create consensus sequences for my BAM files, as suggested on the samtools sourceforge page:...

jeffseq · 03-11-2013, 07:13 AM

Deal all,

How do I get a regional consensus sequence, say ch01: 77295611-77295961, from a BAM file by Samtools?

I extracted...

Himalaya · 10-22-2012, 08:25 AM

Hi All
Do anyone know how Amplicon Variant Analyzer (AVA) make consensus sequence from individual aligned sequences?

kentk · 02-27-2012, 08:50 AM

I wanted to get the consensus sequence from a bam file and came across this
http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SA...

Lspoor · 10-24-2011, 07:19 AM

Hi everyone, I was wondering if you might be able to help me with specifying a minimum read depth when calling consensus sequences?...

PacBio software vcf and consensus fasta do not agree