Sample status

This table gives the status of each sample, either completed successfully or the reason the workflow failed. If applicable the mean quality for the whole plasmid assembly has been provided, derived by Medaka from aligning the reads to the consensus.

The assembly was generated using Flye.
Sample pass/failed reason Length Mean Quality
pGEM_control_barcode92 Completed successfully 3196 31.23

Plannotate

The Plasmid annotation plot and feature table are produced using pLannotate

A pLannotate plot is shown for each assembly. A feature table provides descriptions of the annotated sequence. Unfilled features on the plannotate plots are incomplete features; the sequence match in the plasmid covers less than 95% of the full length of the feature in the database. These elements may be leftover fragments from earlier cloning steps used to create a plasmid. If they include only a small fraction of the feature, they likely do not still have the annotated function. However, even small feature fragments may affect plasmid function if they result in cryptic gene expression or are inadvertently combined with other elements during later cloning steps. The plannotate plot may have overlapping annotation labels, use the zoom and hover tools to decipher the labels.

Feature Database Identity Match Length Description Start Location End Location Length Strand
f1 ori snapgene 100.0% 100.0% f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis 2519 2948 429 +
AmpR promoter snapgene 100.0% 100.0% bla 110 215 105 +
AmpR snapgene 99.8% 100.0% β-lactamase; bla; confers resistance to ampicillin, carbenicillin, and related antibiotics 215 1076 861 +
ori snapgene 99.8% 100.0% high-copy-number ColE1/pMB1/pBR322/pUC origin of replication 1246 1835 589 +
lac promoter snapgene 100.0% 100.0% promoter for the E. coli lac operon 2158 2189 31 +
CAP binding site snapgene 100.0% 100.0% CAP binding activates transcription in the presence of cAMP. E. coli catabolite activator protein 2122 2144 22 +
T7 promoter snapgene 100.0% 100.0% promoter for bacteriophage T7 RNA polymerase 2337 2356 19 -
SP6 promoter snapgene 100.0% 100.0% promoter for bacteriophage SP6 RNA polymerase 2254 2273 19 +
lac operator snapgene 100.0% 100.0% The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG). lac repressor encoded by lacI 2196 2213 17 +
lacZα snapgene 100.0% 90.8% LacZα fragment of β-galactosidase; lacZ fragment 2358 2516 158 +
bom snapgene 100.0% 70.9% basis of mobility region from pBR322 2975 3075 100 -
MCS snapgene 96.5% 100.0% pUC18/19 multiple cloning site 2279 2335 57 -
RNAI Rfam 100.0% 97.1% Accession: RF00106 - RNAI 1285 1390 105 -
T5 promoter snapgene 100.0% 42.2% bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator 2196 2215 19 +
lacI snapgene 100.0% 8.6% lac repressor; lacI; The lac repressor binds to the lac operator to inhibit transcription in E. coli. This inhibition can be relieved by adding lactose or isopropyl-β-D-thiogalactopyranoside (IPTG). 2017 2110 93 +
rop snapgene 100.0% 18.8% Rop protein, which maintains plasmids at low copy number; rop 3176 16 36 -
CMV intron snapgene 100.0% 18.2% modified intron A from human cytomegalovirus (CMV) 2336 2356 20 -
penA swissprot 68.8% 10.2% PENA_BURM1 - Experimental evidence at transcript level: Swiss-Prot protein existence level 2. Upon expression in E.coli enables the latter to utilize penicillin as a carbon source. From Burkholderia multivorans (strain ATCC 17616 / 249). 2108 2204 96 +

Read Counts

Number of reads per sample.

Read stats

For each assembly, read length statistics and plots of quality before and after downsampling, and after host filtering if a host reference was provided.

Completed successfully

Read count

4920

Read count

222

Dot plots

These dot plots have been created by aligning the assembly to itself to reveal any repeats or repetitive regions. Black is for repeats found in the forward strand and red for repeats found in the reverse complement. This was done using last

Workflow Metadata

This table records the data specified in the client fields input.
Key Value
workflow_broker 5.1.10

Software versions

Name Version
medaka 1.11.1
flye 2.9.2-b1786
minimap2 2.26-r1175
samtools 1.18
seqkit v2.5.1
Trycycler v0.5.4
bedtools v2.31.0
fastcat 0.14.1
rasusa 0.7.1
spoa 0.0.10
pandas 1.3.5
plannotate 1.2.0
bokeh 3.1.1

Workflow parameters

Key Value
help False
version False
out_dir /home/grid/epi2melabs/instances/wf-clone-validation_01HSCSZ5HXC5GZ86KANR3WEDW3/output
fastq /data/plasmid_test/plasmid_test/20240313_1227_X5_ANW640_b83748df/fastq_pass/pGEM_control_barcode92
db_directory None
threads 4
host_reference None
regions_bedfile None
approx_size 3500
assm_coverage 60
trim_length 150
prefix None
primers None
insert_reference None
sample None
sample_sheet None
disable_ping False
analyse_unclassified False
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v4.2.0
medaka_model None
flye_quality nano-hq
non_uniform_coverage False
large_construct False
assembly_tool flye
canu_fast False
client_fields /home/grid/epi2melabs/instances/wf-clone-validation_01HSCSZ5HXC5GZ86KANR3WEDW3/client_fields.json
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf
wf {'example_cmd': ['--fastq wf-clone-validation-demo/test', '--primers wf-clone-validation-demo/primers.tsv'], 'container_sha': 'sha840e83632b197d53e8d182e5804ac8429f235d51', 'container_sha_medaka': 'sha61a9438d745a78030738352e084445a2db3daa2a', 'common_sha': 'sha1c5febff9f75143710826498b093d9769a5edbb9', 'container_sha_canu': 'shac3e8468ade9e2b47bf2c4d99ed3e6593a5100c1a', 'agent': 'epi2melabs/5.1.10', 'epi2me_user': 'guest_01HSCSQC5NH4PCN7WYR79AXE26', 'epi2me_instance': '01HSCSZ5HXC5GZ86KANR3WEDW3'}