upload benchmark results

deepomicslab · Aug 4, 2023 · 5b77adf · 5b77adf
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diff --git a/README.MD b/README.MD
@@ -26,7 +26,7 @@ Note:
 
 - SpecHLA requires a License of [Novoalign](https://www.novocraft.com/buy-now/) in `bin/`. If not detected, it uses `bowtie2` as replacement automatically. 
 The License file of `Novoalign` should be put in the `bin/` folder `before` running `bash index.sh`. 
-- SpecHLA now supports Linux and Windows WSL.
+- SpecHLA now supports Linux and Windows WSL systems.
 - SpecHLA does not accept short single-end reads.
 
 
@@ -38,10 +38,10 @@ Please go to the `example/` folder, run SpecHLA with given scripts, and find res
 ### Main functions
 | Scripts | Description |
 | --- | --- |
-|script/ExtractHLAread.sh| Extract HLA reads.|
-|script/whole/SpecHLA.sh| HLA typing with paired-end (PE), PE+long-reads, PE+HiC, or PE+10X data.  |
+|script/ExtractHLAread.sh| Extract HLA reads from enrichment-free data.|
+|script/whole/SpecHLA.sh| HLA typing with paired-end (PE), PE+long reads, PE+HiC, or PE+10X data.  |
 |script/long_read_typing.py|HLA typing with only long-read data.|
-|script/cal.hla.copy.pl|Detect HLA LOH events based on SpecHLA's results.|
+|script/cal.hla.copy.pl|Detect HLA LOH events based on SpecHLA's typing results.|
 
 
 ### Extract HLA-related reads

diff --git a/evaluation/Benchmark_results/Accuracy_Simulate_novel.sequence.xlsx b/evaluation/Benchmark_results/Accuracy_Simulate_novel.sequence.xlsx
diff --git a/evaluation/Benchmark_results/Accuracy_for_IHWG.xlsx b/evaluation/Benchmark_results/Accuracy_for_IHWG.xlsx
diff --git a/evaluation/Benchmark_results/Benchmark_Dataset.xlsx b/evaluation/Benchmark_results/Benchmark_Dataset.xlsx
diff --git a/evaluation/Benchmark_results/Depth_evaluation_wgs.depth.xlsx b/evaluation/Benchmark_results/Depth_evaluation_wgs.depth.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_Pedigree_trio_consistence.xlsx b/evaluation/Benchmark_results/Evaluation_Pedigree_trio_consistence.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_hgsvc.combine_hybrid.xlsx b/evaluation/Benchmark_results/Evaluation_hgsvc.combine_hybrid.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_hgsvc.sequence.xlsx b/evaluation/Benchmark_results/Evaluation_hgsvc.sequence.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_pedigree.sequence.xlsx b/evaluation/Benchmark_results/Evaluation_pedigree.sequence.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_simu.exon.xlsx b/evaluation/Benchmark_results/Evaluation_simu.exon.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_simu.hybrid_long.xlsx b/evaluation/Benchmark_results/Evaluation_simu.hybrid_long.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_simu.sequence.xlsx b/evaluation/Benchmark_results/Evaluation_simu.sequence.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_trio.combine.xlsx b/evaluation/Benchmark_results/Evaluation_trio.combine.xlsx
diff --git a/evaluation/Benchmark_results/Evaluation_trio.simu.xlsx b/evaluation/Benchmark_results/Evaluation_trio.simu.xlsx
diff --git a/evaluation/Benchmark_results/G_group_hybrid_real_data.xlsx b/evaluation/Benchmark_results/G_group_hybrid_real_data.xlsx
diff --git a/evaluation/Benchmark_results/HGSVC2_HIFI.xlsx b/evaluation/Benchmark_results/HGSVC2_HIFI.xlsx
diff --git a/evaluation/Benchmark_results/HGSVC2_PEdata.xlsx b/evaluation/Benchmark_results/HGSVC2_PEdata.xlsx
diff --git a/evaluation/Benchmark_results/HGSVC2_assembly_truth.xlsx b/evaluation/Benchmark_results/HGSVC2_assembly_truth.xlsx
diff --git a/evaluation/Benchmark_results/HGSVC2_truth_G-group typing.xlsx b/evaluation/Benchmark_results/HGSVC2_truth_G-group typing.xlsx
diff --git a/evaluation/Benchmark_results/HLA_database_allele_number.xlsx b/evaluation/Benchmark_results/HLA_database_allele_number.xlsx
diff --git a/evaluation/Benchmark_results/LOH_real_data.xlsx b/evaluation/Benchmark_results/LOH_real_data.xlsx
diff --git a/evaluation/Benchmark_results/SpecHLA_Typing_results_ WGS.1kGenome.xlsx b/evaluation/Benchmark_results/SpecHLA_Typing_results_ WGS.1kGenome.xlsx
diff --git a/evaluation/Benchmark_results/SpecHLA_Typing_results_RNAseq.1kGenome.xlsx b/evaluation/Benchmark_results/SpecHLA_Typing_results_RNAseq.1kGenome.xlsx
diff --git a/evaluation/Benchmark_results/SpecHLA_Typing_results_WES.1kGenome.xlsx b/evaluation/Benchmark_results/SpecHLA_Typing_results_WES.1kGenome.xlsx
diff --git a/evaluation/Benchmark_results/Truth_for_IHWG_Cell_lines.xlsx b/evaluation/Benchmark_results/Truth_for_IHWG_Cell_lines.xlsx
diff --git a/evaluation/Benchmark_results/Typing_evaluation_simu.mode.xlsx b/evaluation/Benchmark_results/Typing_evaluation_simu.mode.xlsx
diff --git a/evaluation/Benchmark_results/Typing_evaluation_simu.software.xlsx b/evaluation/Benchmark_results/Typing_evaluation_simu.software.xlsx
diff --git a/evaluation/readme.md b/evaluation/readme.md
@@ -7,9 +7,10 @@ The scripts to evaluate the typing results are in this folder.
 |cal_resource.py | Calculate the computational resources  |
 |assess_read_assign.py| Evaluate the read-binning accuracy in simulated data |
 |eva_type_accuracy.py| Calculate G-group typing accuracy in real samples |
-|visualize_trio/*| Generate the data format for visulization of trio-consistency |
 |compare.1k.pl |Compare typing results in 1000G samples|
 |get_truth_HSVC2_g.py| Infer G group HLA types from HGSVC2 samples as ground truth|
 |get_HLA_alleles_from_assembly.py| Extract HLA alleles from HGSVC2 samples as ground truth|
 |download_hgsvc_assemly.py| Download phased assemblies of HGSVC2 samples as ground truth |
-|convert.allele.pl | map the HLA types to the most recent IMGT version|
+|convert.allele.pl | map the HLA types to the most recent IMGT version|
+|visualize_trio/*| Generate the data format for visulization of trio-consistency |
+|Benchmark_results/*| Benchmark data collection information and evaluation results |
diff --git a/script/whole/SpecHLA.sh b/script/whole/SpecHLA.sh
@@ -212,7 +212,9 @@ samtools index $outdir/$sample.merge.bam
 
 
 # ################################### local assembly and realignment #################################
-echo start realignment...
+echo "start realignment..."
+echo ""
+echo "Attention: Please ensure the platform can run gzip -l automatically, otherwise, it may not continue."
 if [ $focus_exon_flag == 1 ];then #exon
   assemble_region=$dir/select.region.exon.txt
 else # full length