diff --git a/README.md b/README.md index d357f0a..f156f65 100644 --- a/README.md +++ b/README.md @@ -55,9 +55,9 @@ I like to test bart on SRA reads like so: ``` fastq-dump SRR14224855 --split-files --gzip && bart SRR14224855* ``` -* This completed in 9.6 seconds on a 4-core laptop. +* MLST of these reads completed in 9.6 seconds on a 4-core laptop. -If you already know the species of your reads +If you already know the species of your reads, or the specific scheme you would like to use, you can bypass scheme choosing heuristics. @@ -77,7 +77,7 @@ Now you can run: ``` bart SRR14224855* -s Staphylococcus_aureus ``` -Output is now a single tab-separated line . +Output is now a single tab-separated line. Alleles are presented like so: * gene(allele), where the allele is from the matching, or nearest matching profile. * '?' indicates a non-perfect hit @@ -89,16 +89,18 @@ Alleles are presented like so: Verbose `-v` prints the top hit allele in square brackets next to the allele number if different from the profile allele. -Alternative allele hits that were also found will also be printed. +Alternative allele hits that were found will also be printed. This means you can make an informed decision about the ST if there are several near-profile assignments. | SRR14224855 | Staphylococcus_aureus | 9 | arcC(3)346,616 | aroE(3)260,415 | glpF(1) | gmk(1)85 | pta(1)777 | tpi(1)269 | yqiL(10)816 | clonal_complex(CC1) | |-------------|-----------------------|---|-------------------------------------|-------------------------------------|------------------------------|-------------------------------|--------------------------------|--------------------------------|----------------------------------|---------------------| -"Verboser" `-vv` does the same, but prints mapping data of the top hit in the following format: -gene(allele: %identity, %coverage, depth) alternative alleles +"Verboser" `-vv` does the same, but prints mapping data +of the top hit in the following format: +`gene(allele: %identity, %coverage, depth) alternative alleles` + or if the top allele hit isn't the same as the assigned profiles: -gene(allele)[top hit allele: %identity, %coverage, depth] alternative alleles +`gene(allele)[top hit allele: %identity, %coverage, depth] alternative alleles` | SRR14224855 | Staphylococcus_aureus | 9 | arcC(3: 100.00 100.00 40.52)346,616 | aroE(3: 100.00 100.00 27.58)260,415 | glpF(1: 100.00 100.00 27.84) | gmk(1: 100.00 100.00 24.42)85 | pta(1: 100.00 100.00 36.66)777 | tpi(1: 100.00 100.00 52.26)269 | yqiL(10: 100.00 100.00 44.92)816 | clonal_complex(CC1) | |-------------|-----------------------|---|-------------------------------------|-------------------------------------|------------------------------|-------------------------------|--------------------------------|--------------------------------|----------------------------------|---------------------|