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CMU-SAFARI / Apollo

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-assembly-polishing_bioinformatics20.pdf
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illumina paire-end reads #2

Closed SC-Duan closed 5 years ago

SC-Duan commented 5 years ago

Hi, I just have illumina pair-end reads, can I cat the R1.fa and R2.fa together as reads.fa to do polish? Thank you!

canfirtina commented 5 years ago

Hello,

Yes, it is possible to use the paired-end reads as you suggested. Please also make sure that the ids of the two pairs are not identical in reads.fa file (e.g., having both >pair_1/1 and pair_1/2 in reads.fa is OK but pair_1 /1 and pair_1 /2 is not OK because the ids of the both reads are pair_1).

SC-Duan commented 5 years ago

Thank you!