Opis
Bionano Solve je skup alata za analizu Bionano podataka (generiranih od Saphyr i Irys)
Dostupne verzije
| Verzija | Modul | Supek | Padobran |
|---|
| 3.8.2 | scientific/bionano-solve/3.8.2 |  |  |
Dokumentacija
Bionano solve se sastoji od mnoštvo skripti i izvršnih datoteka. Sadržaj nekih je opisan niže.
Popis direktorija u putanji /tools/pipeline/1.0/
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $EnFocus_Repeats |
|---|
| collapse | true |
|---|
|
GMM
README.md
configs.py
enfocus-repeat-expansions-azure-pipelines.yml
enfocus_repeat.py
enfocus_repeat_utilities.py
enfocus_zip_and_manifest.py
finalize_data.py
hg38_DLE1_fmr1_stableRegions.cmap
mol_to_map.py
prior_copies
read_qry_interval.py
realign_sites.py
repeat_bayes_model.py
repeat_coords.csv
reporting.py
run_enfocus_repeat.py
smith_waterman.py |
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $FSHD |
|---|
| collapse | true |
|---|
|
Extract_mols.py
FSHD_analysis.py
FSHD_utilities.py
README.md
assess_by_groundtruth.py
check_FSHD_bnx_file.py
check_ambiguous_map_align.py
chimeric_check.py
cnv_data.py
configs.py
fshd-azure-pipelines.yml
identify_anchor.py
identify_hap.py
load_data.py
map_quality_control.py
molecule_quality_data.py
prepare_map_data.py
read_xmap_refaligner.py
repeat_integrity_check.py
reporting.py
resources
run_FSHD_analysis.py |
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $Hybrid_Scaffold |
|---|
| collapse | true |
|---|
|
AssignAlignType.pl
ExportAGP.pl
ExportAGP_TwoEnzyme.pl
MergeNGS_BN.pl
align_final_bng.pl
align_final_seq_two_passes.pl
align_molecules.pl
calc_chim_score.pl
calc_cmap_stats.pl
calc_conflicts_cut_stats.pl
calc_fasta_stats.pl
calc_hybrid_scaffold_not_scaffolded_seq_fasta_stats.pl
calc_scaffolded_seq_fasta_stats.pl
calc_xmap_stats.pl
cut_conflicts.pl
estimate_cmap_stats.pl
estimate_fasta_stats.pl
estimate_hybrid_scaffold_input_stats.pl
fa2cmap_multi_color.pl
fa_key_convert.pl
fasta_filter.py
find_used_not_used_bn.pl
find_used_not_used_ngs.pl |
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $Pipeline |
|---|
| collapse | true |
|---|
|
Pipeline.py
align_bnx_to_cmap.py
alignment.py
assemble.py
autonoise.py
bam_conversion.py
batch_cleanup
bnx.py
characterize.py
clusterArguments.xml
clusterArgumentsBG.xml
clusterArgumentsBG2_aws.xml
clusterArgumentsBG3_aws.xml
clusterArgumentsBG_3100.xml
clusterArgumentsBG_aws.xml
clusterArgumentsBG_nfs1.xml
clusterArgumentsBG_saphyr_phi.xml
clusterArgumentsHC.xml
clusterArgumentsHC_nfs1.xml
clusterArguments_3100.xml
clusterArguments_7100.xml
clusterArguments_Amber.xml
clusterArguments_Carbon.xml
clusterArguments_access.xml
clusterArguments_aws.xml
clusterArguments_awsC5n.xml
clusterArguments_awsM5.xml
clusterArguments_awsR5.xml
clusterArguments_aws_batch.xml
clusterArguments_nfs1.xml
clusterArguments_saphyr.xml
clusterArguments_saphyr4.xml
clusterArguments_saphyr4_slurm.xml
clusterArguments_saphyr_phi.xml
clusterArguments_saphyr_slurm.xml
clusterArguments_saphyr_supermicro.xml
clusterArguments_saphyr_supermicro_slurm.xml
clusterArguments_stratys_slurm_constitutional_3gpu.xml
clusterArguments_stratys_slurm_constitutional_4gpu.xml
clusterArguments_stratys_slurm_laf_3gpu.xml
clusterArguments_stratys_slurm_laf_4gpu.xml
cmap.py
cnv.py
confidencescores.py
config.py
definitions.py
extract_mols.py
filetypes.py
fileutils.py
grouped_refinement.py
lohdetection_pipeline.py
mapClasses.py
merging.py
mthreading.py
pairwise.py
pipelineCL.py
pipeline_script_template.sh
reports.py
runAlignMol.py
runCharacterize.py
runSV.py
run_targeted_assembly.py
svdetect.py
utilities.py
vaf_pipeline.py
vap_alignmol.py
vap_caller.py
varcluster.py |
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $SVviewer |
|---|
| collapse | true |
|---|
|
Visualize_inversions.pl |
Također izvršne datoteke su dodane u $PATH, popis se nalazi niže.
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | $PATH izvršne datoteke |
|---|
| collapse | true |
|---|
|
checkMPS.sh
clusterArguments_Graphite.xml
clusterArguments_Titanium.xml
compressPipeline.sh
filter_SNR_dynamic.pl
irys_db_tool.R
runDenovo
run_aws
runpipe
variant_clustering
Assembler
RefAligner
ColorSplit.pl
MQR.pl
V3_Cohort_QC.pl
demultiplex.sh
filter_SNR_dynamic.pl |
Primjer
- Odabir cpu-a i mem proizvoljno, ovisi o skripti
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | RefAligner |
|---|
|
#PBS -N bionano-test
#PBS -l select=1:ncpus=12:mem=20GB
#PBS -q cpu
cd $PBS_O_WORKDIR
module load scientific/bionano-solve/3.8.2
bionano.sh RefAligner -i autoNoise1_rescaled.bnx -randomize 1 -subset 1 15000000 -merge -o output -bnx -maxthreads $NCPUS -maxmem 20 |
| Code Block |
|---|
| language | bash |
|---|
| theme | Midnight |
|---|
| title | filter_SNR_dynamic |
|---|
|
#PBS -N bionano-test
#PBS -l select=1:ncpus=2:mem=8GB
#PBS -q cpu
cd $PBS_O_WORKDIR
module load scientific/bionano-solve/3.8.2
bionano.sh filter_SNR_dynamic.pl -i autoNoise1_rescaled.bnx -o output_filter_SNR |
| Warning |
|---|
|
Ako postoji opcija odabira dretvi u skripti, moguće da će biti različiti, stoga je potrebno provjeriti u dokumentaciji i/ili u samom -help/priručniku skripte npr.
module load scientific/bionano-solve/3.8.2
bionano.sh RefAligner -help
|
