Security scan: 10 of 57 tools have vulnerabilities - 2026-08-16

[github-actions]

Trivy Security Scan Results - 2026-08-16

Summary

• Tools scanned: 57
• Tools with vulnerabilities: 10
• Total CRITICAL + HIGH vulnerabilities: 642

Per-Tool Results

Tool	Versions	CRITICAL	HIGH
abacas	1	0	0
abismal	1	0	0
abpoa	1	0	0
abricate	2	8	129
abyss	1	19	73
actc	1	0	0
adapterremoval	2	0	0
advntr	1	1	28
afplot	1	21	68
afterqc	1	0	6
agat	2	0	0
agfusion	2	0	38
alevin-fry	5	0	0
alfred	2	0	0
alien_hunter	1	29	140
alignstats	1	0	0
alphafold	1	14	120
alphafold3	1	21	372
amplican	1	0	3
amptk	1	3	36
ananse	1	3	40
anchorwave	1	0	0
angsd	1	0	0
anndata2ri	2	0	1
annogesic	1	4	137
annovar	2	44	634
antarna	1	1	9
antismash	1	0	17
anvio	1	43	238
any2fasta	1	0	0
arboreto	1	0	27
arcs	1	0	4
ariba	1	19	88
arriba	1	0	2
ascatngs	1	2	201
asgal	1	0	4
ashlar	2	0	47
aspect	1	21	356
assembly-stats	1	0	0
atac-seq-pipeline	1	4	16
ataqv	1	0	4
atropos	1	0	3
augur	7	7	161
augustus	1	0	0
bactopia	2	3	85
bali-phy	2	0	0
bam-readcount	1	0	0
bamgineer	1	1	94
bamliquidator	1	0	25
bamscale	1	0	0
bamsurgeon	1	0	5
bamtools	1	0	0
bamutil	1	0	0
bandage	1	19	70
baredsc	2	2	42
barrnap	2	0	0
basenji	1	3	82
bases2fastq	1	34	681
bayescan	2	0	0
bazam	1	6	13
bbmap	1	0	0
bcftools	7	0	0
bcl2fastq	1	12	81
beast2	1	1	1
bedops	1	0	0
bedtools	3	0	0
bioawk	1	0	0
biobambam	1	0	0
bioconvert	1	43	432
bismark	1	0	0
blasr	1	0	7
blast	1	0	0
blobtools	1	3	15
blockbuster	1	0	0
bmge	1	0	0
bowtie	1	0	4
bowtie2	4	0	11
bracken	1	3	48
braker3	1	16	172
brass	1	0	6
breseq	1	0	0
busco	4	113	674
bustools	1	0	0
bwa-mem2	3	0	0
bwa	1	0	0
bwameth	1	0	0
cactus	2	0	77
cafe	1	0	0
canu	1	19	74
cd-hit	1	0	0
cellbender	1	5	43
cellranger-arc	1	90	725
cellranger-atac	1	87	659
cellranger	1	56	454
cellrank-krylov	1	4	31
cellrank	1	4	31
cellsnp-lite	1	0	0
celltypist	1	0	22
cemitool	1	0	3
centrifuge	1	0	0
checkm-genome	1	0	12
checkv	1	6	59
chewbbaca	2	2	34
chipseeker	1	0	3
chopper	2	0	0
chromap	1	0	0
cicero	1	0	0
circexplorer2	1	1	9
circlator	1	0	11
circompara2	1	2	219
circos	1	0	0
ciriquant	1	0	3
cite-seq-count	1	0	17
clair3	2	38	146
clairvoyante	1	4	121
clearcnv	1	4	51
clever-toolkit	1	0	13
clonalframeml	2	0	0
cnvkit	3	0	29
cnvnator	1	0	13
coinfinder	1	0	4
concoct	1	0	2
control-freec	1	0	3
cooler	1	19	99
cosg	2	0	29
coverm	2	0	0
cramino	1	0	0
crisprcasfinder	1	0	0
crispresso2	1	0	10
crispritz	1	0	23
crossmap	1	0	3
cryptogenotyper	1	0	4
csvtk	1	1	37
cufflinks	1	0	6
cummerbund	1	0	3
cutadapt	1	0	0
cutesv	1	0	3
cuttlefish	1	0	0
cyvcf2	2	0	0
datamash	1	0	0
dbg2olc	1	0	0
debreak	1	0	4
deepbgc	1	6	130
deepconsensus	1	52	339
deeptools	1	0	22
deepvariant	4	15	373
delly	4	0	0
dendropy	2	0	0
deseq2	3	0	5
dexseq	1	0	3
diamond	2	0	0
diffbind	1	0	3
dnaapler	2	0	0
dnaio	2	0	0
dragonflye	1	8	101
drep	2	4	36
dropest	1	0	7
dss	1	0	0
dsuite	1	258	2452
edger	1	0	0
edta	1	5	107
eggnog-mapper	2	38	143
egsea	1	0	3
emboss	1	4	5
enrich2	1	29	438
ensembl-vep	1	1	18
epic2	1	0	3
episcanpy	1	1	23
ete	1	1	9
evidencemodeler	1	0	0
exomedepth	1	0	2
exonerate	1	0	0
expansionhunter	1	0	0
express	1	0	0
falco	5	0	0
fastani	1	0	0
fastp	2	0	0
fastq-dl	2	0	0
fastq-scan	1	0	0
fastq_pair	1	0	0
fastq_utils	1	0	0
fastqc	3	0	0
fastspar	1	0	0
faststructure	1	0	12
fasttree	1	0	0
feelnc	1	0	0
filtlong	1	0	0
flaimapper	1	1	9
flye	1	0	3
fq	1	0	0
fraggenescan	1	0	0
fraggenescanrs	1	256	2518
freebayes	1	0	0
freyja	1	1	36
fuma	1	1	8
funannotate	1	2	37
fwdpy11	1	0	5
gadma	1	0	31
gambit	1	0	0
gamma	1	0	0
gangstr	1	0	0
gapfiller	0	0	0
gatk4	3	20	134
gcta	0	0	0
gecko	1	0	0
gemma	0	0	0
gemoma	0	0	0
genmap	0	0	0
genomepy	0	0	0
genomescope2	0	0	0
genomicconsensus	0	0	0
genomicsupersignature	1	0	3
genrich	0	0	0
getorganelle	1	6	59
gfaffix	0	0	0
gfastats	1	19	70
gfatools	0	0	0
gffcompare	0	0	0
gffread	0	0	0
gffutils	0	0	0
gimmemotifs	0	0	0
glimmerhmm	0	0	0
glnexus	0	0	0
gmap	0	0	0
goatools	0	0	0
goseq	1	0	3
graphlan	0	0	0
graphmap	0	0	0
graphprot	2	1	9
gridss	0	0	0
gromacs	0	0	0
gseapy	0	0	0
gtftools	0	0	0
gubbins	1	0	3
hail	0	0	0
hamronization	2	0	0
hapo-g	1	0	2
hclust2	0	0	0
heinz	1	0	0
helen	0	0	0
hgvsparser	1	0	0
hic-pro	1	3	43
hicexplorer	1	0	33
hicup	1	19	202
hifiasm	1	0	0
hisat2	1	0	0
hmmer	1	0	0
homer2	1	0	0
homopolish	1	0	9
htseq-clip	1	1	18
htseq	1	0	16
htslib	1	0	0
htstream	1	0	0
humann	1	12	160
hybpiper	2	5	105
hyphy	4	76	280
hypo	1	0	0
idba	1	0	0
igv	1	0	11
impute2	1	0	0
infercnv	1	0	3
infernal	1	0	0
instrain	1	0	22
intarna	1	0	3
interproscan	1	39	262
ipyrad	1	1	36
isescan	1	3	48
ismapper	1	1	8
isoformswitchanalyzer	1	0	3
isoquant	1	0	2
ivar	1	0	0
jamm	1	0	0
jasmine	1	0	4
kaiju	1	0	0
kallisto	4	0	0
kentutils	0	0	0
khmer	0	0	0
kissplice	0	0	0
kma	0	0	0
kmc	0	0	0
kmer-jellyfish	0	0	0
kmergenie	0	0	0
kneaddata	0	0	0
kofamscan	1	2	11
kover	0	0	0
krakentools	0	0	0
lambda	0	0	0
last	0	0	0
lastz	1	0	0
ldhat	0	0	0
ldsc	0	0	0
legsta	1	0	0
liftoff	0	0	0
liftofftools	0	0	0
liger	1	0	0
lima	0	0	0
limma	1	0	0
links	1	0	0
locarna	1	0	3
lofreq	1	0	4
longphase	0	0	0
longqc	0	0	0
lorikeet	1	0	0
lra	0	0	0
ltr_finder	0	0	0
ltrpred	0	0	0
lumpy-sv	1	0	7
macrel	0	0	0
macs3	4	0	10
mafft	3	9	93
mageck	1	0	3
maker	1	0	3
manta	1	0	6
mashmap	1	0	0
masigpro	1	0	0
megahit	1	0	0
methylkit	1	0	3
minced	1	0	0
minfi	3	0	9
minia	1	0	0
minipolish	2	0	3
mirdeep2	1	0	4
mitos	1	0	16
mummer	1	2	6
muscle	1	0	0
music	1	0	0
nastiseq	1	0	0
nextclade	4	0	0
odgi	2	0	0
optitype	2	2	29
pacu	2	1	102
pangolin	2	4	99
pbmm2	3	0	0
peakachu	1	1	20
peakzilla	1	0	7
pharmcat3	3	0	5
phyml	3	0	0
picrust2	2	3	31
pilon	1	0	6
piranha	1	0	0
pizzly	2	0	0
plink2	3	0	0
prokka	1	4	66
psiclass	1	0	0
psortb	1	0	49
qualimap	1	1	7
quast	1	22	134
raceid	1	0	5
racon	1	0	0
ragtag	1	2	28
raven-assembler	1	0	0
raxml	1	0	0
rbpbench	3	3	99
rcas	1	0	3
repeatmasker	1	3	48
repeatmodeler	2	5	81
ribotaper	1	0	0
ribowaltz	1	0	3
rnacode	1	0	0
rnashapes	1	0	0
roary	1	0	6
rsem	1	0	0
rseqc	1	0	19
ruvseq	1	0	3
sailfish	1	0	7
salmon	2	0	0
salsa	1	0	6
samtools	5	0	0
scanpy	1	56	832
scater	1	0	3
sceasy	1	0	3
scpipe	1	0	3
scran	1	0	2
seq2hla	1	0	7
seurat	1	22	388
shasta	1	0	0
sicer	1	1	7
sina	1	0	6
sinto	1	0	15
sleuth	1	0	0
smudgeplot	1	0	13
snapatac	1	0	10
sniffles	4	0	6
snpeff	3	20	76
snpsift	1	0	4
sonneityping	1	0	4
sopa	6	0	189
spades	1	0	0
spapros	2	0	101
spotyping	1	0	7
squirrel	2	2	95
ssake	1	0	7
star	3	0	0
strelka2	3	0	20
stringtie	2	0	0
t-coffee	1	1	18
targetfinder	1	0	0
tgs-gapcloser	1	0	0
tiddit	1	0	3
tophat	1	0	2
transdecoder	1	0	0
transit	2	0	34
treebest	1	0	0
trimal	1	0	0
trinity	1	1	2
trinotate	1	0	7
trycycler	1	0	16
tximport	1	0	0
usher	1	20	89
vardict	1	0	0
varscan	1	0	0
vcfanno	2	0	0
vcflib	2	0	0
velocyto	1	19	85
vg	1	0	0
viennarna	2	0	4
vt	1	0	0
winnowmap	1	0	0
wtdbg2	1	0	0

What to do

1. Review the trivy-scan-results.json files for each affected tool
2. Prioritise CRITICAL vulnerabilities for immediate remediation
3. Plan container image updates for affected versions

Automated by Trivy Security Scan