From the FRCurve directory run:
You will find the binaries in the main directory under bin. In case of problems the majority of the times there is a problem with the local installation of boost.
FRCbam is a tool able to evaluate and analyze de novo assembly/assemblers. The tool has been already successfully applied in several de novo .
FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers
USAGE: basic, no CE-stats tuning
--genome-size ESTIMATED_GENOME_SIZE --output OUTPUT_HEADER```
where:
--pe-sam
A_tool1_PE_lib.bam```: sorted bam file obtained aligning PE library against assembly obtained with tool A;--pe-min-insert MIN_PE_INS
: estimated min insert length--pe-max-insert MAX_PE_INS
: estimated max insert length--mp-sam A_tool1_MP_lib.bam
: sorted bam file obtained aligning MP library against assembly obtained with tool A;--mp-min-insert MIN_MP_INS
: estimated min insert length--mp-max-insert MAX_MP_INS
: estimated max insert length--genome-size ESTIMATED_GENOME_SIZE
: estimated genome size;--output OUTPUT_HEADER
: output header;IMPORTANT:
If --genome-size
is not specified the assembly length is used to compute FRCurve. In order to be able to compare FRCurves
obtained with different tools (and hence producing slightly different assembly sizes) the same ESTIMATED_GENOME_SIZE
must be specified.
OUTPUT:
OUTPUT_HEADER_Features.txt
: human readable description of features: contig start end feature_typeOUTPUT_HEADER_FRC.txt
: FRCurve computed with all the features (to be plotted)OUTPUT_HEADER_FEATURE.txt
: FRCurve for the corresponding featureOUTPUT_HEADER_featureType.txt
: for each featureType the specific FRCurveFeatures.gff
: features description in GFF format (for visualization)OUTPUT_HEADER_CEstats_PE.txt
: CEvalues distribution (for CE_stats tuning)OUTPUT_HEADER_CEstats_MP.txt
: CEvalues distribution (for CE_stats tuning)USAGE: advanced, CE-stats tuning
CE-stats are able to identify the presence of insertion and deletion events. Different insert sizes give the possibility to identify different events. In order to avoid too many False Positives (or too many False Negatives) a tuning phase is highly recommended.
Once step 3 of USAGE is done, the user can already plot the FRCurves (for all the features or for only some of them).
CE_stats based features have been computed with default (i.e., not optimal) parameters. Each run of FRCbam produces two
files: OUTPUT_HEADER_CEstats_PE.txt
and OUTPUT_HEADER_CEstats_MP.txt
. These files contain the distribution of the CE_values
on each assembly. These values must be plotted as suggested in page 3 of Supplementary Material
(see http://www.nada.kth.se/~vezzi/publications/supplementary.pdf) to estimate the optimal CE_min
and CE_max
values for
the PE and MP library respectively.
Once the optimal parameters are estimated FRCurves must be recomputed for all assemblies (only COMPR
and STRECH
features
will change) specifying the following extra parameters:
--CEstats-PE-min CE_PE_MIN
: all position with CE values computed with PE library lower than this are considered compressions--CEstats-PE-max CE_PE_MAX
: all position with CE values computed with PE library higher than this are considered expansions --CEstats-MP-min CE_MP_MIN
: all position with CE values computed with MP library lower than this are considered compressions--CEstats-MP-max CE_MP_MAX
: all position with CE values computed with MP library higher than this are considered expansionsAll the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).