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SMRT Link 7.0 - HGAP
Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all.... -
HGAP and PBcR self-correction
I'd like to know about difference between HGAP and PBcR self-correction.
Both pipelines perform DeNovo assembly by using PacBio reads only.
...Last edited by kende; 05-28-2015, 02:46 AM. -
Best parameter for bacteria de novo assembly - HGAP
Hello,
I would like to know what is best for bacteria genome assembly in general. I work on 4M~6M genomes in general and they have 1 or 2...Last edited by heyyyjude; 05-23-2015, 08:36 PM. -
HGAP command line protocol ?
Hello everyone,
I'm new to PacBio so I need your help to guide me or give me some suggestions on my de novo assembly project. I'm currently... -
lowercase output from quiver
I recently completed resequencing of a bacterial strain with a complete reference genome. The HGAP3 assembly resulted in a single contig, but there were... -
Low Pre-Assembly yield in HGAP2
I'm noticing surprisingly low pre-assembly yields for an HGAP 2.2 run on a small bacteriophage genome (~150kb). Depending mostly on the min seed read... -
PacBio internal control showing up in polished HGAP assembly
I noticed something odd when running two different HGAP assemblies. In both cases, the polished_assembly.fasta files contained a ~4kb contig with >3000x... -
HGAP issue in smrtanalysis 2.0.1
I'm trying to assemble a bacterial genome (about 4.1Mbases in length) using HGAP in smrtanalysis 2.0.1. The job runs until the draft assembly is finished... -
HGAP Parameters in SMRT Analysis
Hello,
We just got SMRT Analysis installed in our lab and are trying to use HGAP for the first time. We have uploaded a SMRT cell into...
