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wangna62691 / PacBio_Assembly

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Pacbio_Final #5

Open wangna62691 opened 7 years ago

wangna62691 commented 7 years ago

•Develop your final analysis script and XML files in GitHub, and in a new issue on github: • record link to xml file settings.xml: https://github.com/wangna62691/PacBio_Assembly/blob/master/settings.xml settings_motif_ecoli.xml: https://github.com/wangna62691/PacBio_Assembly/blob/master/settings_motif_ecoli_2.xml

• record link to final analysis script https://github.com/wangna62691/PacBio_Assembly/blob/master/Pacbio_final_pipeline • record exact command used to submit job

qsub -q rcc-30d -l mem_total=8g -pe thread 4 ./pacbio_pipeline.sh

• record GitHub revision of script used https://github.com/wangna62691/PacBio_Assembly/blob/a07ba2122103e86e13fc84a1e5c645e9d0535860/Pacbio_final_pipeline

• link to all previous issues where you developed components of pipeline Canu assembly: https://github.com/wangna62691/PacBio_Assembly/issues/2 Polishing and pokka: https://github.com/wangna62691/PacBio_Assembly/issues/3 Modification analysis: https://github.com/wangna62691/PacBio_Assembly/issues/4

cbergman commented 7 years ago

Report is correct and mostly complete, with the exception of the quantification of how polishing improves the genome assembly. This section should have included information from Quast reports vs. the reference sequence and a comparison of Prokka gene numbers before and after polishing. This would show that the SNP and especially indel error rate goes down after polishing, and the number of gene models also goes down since indels no longer cause frameshifts which break gene models. Scripts, XMLs and issue are complete. Overall, nice job!