prooveval --help # option details
prooveval [<OPTIONS>] --ref <genome.fa> --qry <reads.fa> --gmap-sry <reads.sry> [--uncorrected <raw-reads.fa>]
# with progress
pv <reads.sry> | prooveval [<OPTIONS>] --ref <genome.fa> --qry <reads.fa> --gmap-sry - [--uncorrected <raw-reads.fa>]
# generate gmap summary
gmap -b -B 5 -O -Y -K 9 -w 9 --align [-t 32] -D /gmap_db/dir -d gmap_db_name reads.fa > gmap.srygit clone --recursive https://github.com/BioInf-Wuerzburg/prooveval.gitprooveval first maps query reads with GMAP. In details, mapping statistics are
listed for different categories. Only the first path (p0 = best hit) is
analysed. Individual stats are available depending on the total amount of paths
returned (:1 - :5 or more), as ambiguously mapped reads are more likely to
produce less accurate correction results. Also chimeric mappings, mappings
extending past reference contig ends and of course unmapped reads are listed
separately.
After inital mapping, all non-chimeric/non-edge-mappings, category gmap_p0:1-5
are checked for full-length mappings (bypass). Partial mappings are realigned
to the region of the hit using exonerate (exo_preref ->
exo_refined). Full-length alignments are important, as in particular sequence
ends tend to carry more errors, and hence dropped ends will affect accuracy
assessment.
Final accuracy is determined as the percentage of matches compared to total
aligned bases of alignments that have either been refined or bypassed the
full-length filter (exo_re+by).
| key | description |
|---|---|
| %bp:unc | percentage of base pairs in comparion to uncorrected input |
| bp:N50 | N50 in base pairs |
| %ma/to | percentage of matches compared to total base pairs in category |
| bp:match | number of matches |
| bp:mm | number of mismatches |
| bp:de | number of deletions |
| bp:in | number of insertions |
| bp:dr | number of dropped bases at the end of alignments |
ref: reference.fa cor: proovread_run.050X_final.corr.fil.fa unc: input_pacbio.fa category R_used R_total bp:total %bp:unc bp:N50 %ma/to bp:match bp:mm bp:de bp:in bp:dr --summary-------------------------------------------------------------------------------------------------------- in_uncorrected 50765 55666 98213822 100.00 4082 -NA- 0 0 0 0 0 exo_uncorrecte 0 55666 -NA- -NA- -NA- -NA- 0 0 0 0 0 in_corrected 55666 55666 76765456 78.16 2206 -NA- 0 0 0 0 0 exo_re+by 55371 55666 76231506 77.62 2202 99.974 76214948 11333 2011 6786 0 --details-------------------------------------------------------------------------------------------------------- gmap_unmapped 70 55666 32156 0.03 1666 -NA- 0 0 0 0 0 gmap_chimera 219 55666 491780 0.50 3157 97.884 481409 597 0 50 9758 gmap_edge_mapp 6 55666 10014 0.01 1884 -NA- 0 0 0 0 0 gmap_multi_exo 0 55666 -NA- -NA- -NA- -NA- 0 0 0 0 0 gmap_p0:1 52222 55666 72062164 73.37 2213 99.970 72042057 2703 0 2628 16048 gmap_p0:1-5 55371 55666 76231506 77.62 2202 99.954 76198144 5631 0 3202 26009 gmap_p0:2 1808 55666 2616289 2.66 2177 99.921 2614315 1555 0 247 259 gmap_p0:3 576 55666 861982 0.88 2262 99.230 855398 927 0 211 5502 gmap_p0:4 261 55666 296322 0.30 1621 99.864 295943 194 0 34 175 gmap_p0:5 504 55666 394749 0.40 1316 98.896 390431 252 0 82 4025 exo_bypass 54925 55666 75690475 77.07 2203 99.989 75684062 4868 0 3106 0 exo_preref 446 55666 541031 0.55 2017 95.033 514082 763 0 96 26009 exo_refined 446 55666 541031 0.55 2017 97.761 530886 6465 2011 3680 0 ----------------------------------------------------------------------------------------------------------