Lrefinder report - Githubissues

NMRL / Ardetype

Pipeline allows to perform reference-guided de-novo assembly of bacterial genomes, starting from Illumina PE150 fastq files.

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Lrefinder report #12

Closed omegatro closed 1 year ago

omegatro commented 1 year ago

Added aggregation script for lrefinder results. Currently the LRE-Finder database contains only two resistance-conferring mutations for E.faecalis and E.faecium: 23S RNA G2505A and G2576T. The thresholds to infer resistance from reads is set to at least 10% of reads containing mutant type (default setting, configurable in db-lrefinder/elm.mutdist). The results are aggregated in the following form:	sample_id	batch_id	#Template	pos	ref	A	C	G	T	N	-	A[%]	C[%]	G[%]	T[%]	N[%]	-[%]
---------	--------	----------	---	---	-	-	-	-	-	-	----	----	----	----	----	----

Template : name of the sequence in the database
pos : position number
ref : reference base
A:count of reads with A at pos
C : count of reads with C at pos
G : count of reads with G at pos
T : count of reads with T at pos
N : count of reads with N at pos
- : count of reads with: at pos
A[%]: fraction of reads with A at pos
C[%]: fraction of reads with C at pos
G[%]: fraction of reads with G at pos
T[%]: fraction of reads with T at pos
N[%]: fraction of reads with N at pos
-[%]: fraction of reads with: at pos

Tested on:

230510_NDX550703_RUO_0076_AHCWJVBGXT
Closes #5
References
https://bitbucket.org/genomicepidemiology/lre-finder/
https://cge.food.dtu.dk/services/LRE-finder/