How practically to produce a whole genome contig from the short reads of M tuberculosis?
How practically to produce a whole genome contig from the short reads of M tuberculosis? How many of short reads are required if they are from the online database or from the local sequencing machine? Is a pair of fastqs enough to make a contig?
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By assembling the data you have. Generally for bacterial genomes SPAdes is the assembler of choice. Having long read PacBio data of sufficient size/quality is known to lead to single contig assemblies.
It should not matter where the data came from you would still need an adequate amount. Higher the coverage (in terms of raw bases) the better but 25x and above is probably advisable. Depends to some extent on the quality of your libraries.
Yes .. if they have enough data in them (ref above).
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