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bhattlab / lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

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using fastq file as initial input file

hites77 opened this issue · comments

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Hi, i found this program very appropriate for assembling bacterial genome from both long and short reads (genome sequence data only and not metagenome). Can you help me how can I run the program when the initial file I have is fastq file rather than fast5 file ? As i try to remove the basecalling function but it is giving error at later stages. I didnt have enough knowledge of snakemake rules and calling. Also which steps can be removed if its single genome sequence data and not metagenome.