search

Gabaldonlab / redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
GNU General Public License v3.0
129 stars 20 forks source link

Assembly correction #84

Closed mamtamasand closed 3 years ago

mamtamasand commented 3 years ago

Hello everyone I am trying to assemble 1.3Gb genome with 1.2% heterozygosity. I have done the hybrid assembly with masurca which resulted to overestimated assembly, the i ran redundans program which gives the assembly of 1GB, reduced size from actual genome size. In the result folders there are two corrected files, intially i got the 1.4GB assembly with gap closing with long reads and after that 1GB with mapping short reads. My question is, Can I use the 1.4GB assembly named as scaffolds.longreads.1.fa for downstream data analysis, because I am worried that in final 1GB assembly from redundans i will miss the gene models. Please suggest the more appropriate way. Thank You in advance

lpryszcz commented 3 years ago

Hi, have you used long reads with redundans?

yes, you can definitely use the scaffolds.longreads.1.fa. Just keep in mind that it skips the last reduction step. Still, the initial heterozygous contigs should be removed before scaffolding.

mamtamasand commented 3 years ago

ok Thank You

On Mon, Mar 15, 2021 at 3:44 PM Leszek Pryszcz @.***> wrote:

Hi, have you used long reads with redundans?

yes, you can definitely use the scaffolds.longreads.1.fa. Just keep in mind that it skips the last reduction step. Still, the initial heterozygous contigs should be removed before scaffolding.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lpryszcz/redundans/issues/84#issuecomment-799296675, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJBFQDIJ4CPGOUCZV25NAJTTDXMXBANCNFSM4ZBRSD4A .