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A safe place for the personal scripts used in the long-read benchmarking project.

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GPL-2.0 license
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shaniAmare/long_read_benchmark_project_scripts

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5 Commits
metrics-sts-master
metrics-sts-master
 
 
stsPlots-master
stsPlots-master
 
 
.gitignore
.gitignore
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
alignqc_ont.bash
alignqc_ont.bash
 
 
alignqc_pacbio.bash
alignqc_pacbio.bash
 
 
bambu.R
bambu.R
 
 
check_results_isophase.bash
check_results_isophase.bash
 
 
fastqc_pacbio.bash
fastqc_pacbio.bash
 
 
featureCounts.r
featureCounts.r
 
 
flair_pacbio_all.bash
flair_pacbio_all.bash
 
 
flair_pacbio_merged.bash
flair_pacbio_merged.bash
 
 
flair_pacbio_merged_final.bash
flair_pacbio_merged_final.bash
 
 
flair_pacbio_merged_new.bash
flair_pacbio_merged_new.bash
 
 
flair_pacbio_merged_q_p_ir.bash
flair_pacbio_merged_q_p_ir.bash
 
 
flames_pacbio_merged.bash
flames_pacbio_merged.bash
 
 
generalqc_pacbio_ccs.bash
generalqc_pacbio_ccs.bash
 
 
gzip_fastq.bash
gzip_fastq.bash
 
 
isophase_pacbio_merged_ref.bash
isophase_pacbio_merged_ref.bash
 
 
longqc_pacbio.bash
longqc_pacbio.bash
 
 
nanoplot_pacbio.bash
nanoplot_pacbio.bash
 
 
picardtools_insertsize_pacbio_ccs.bash
picardtools_insertsize_pacbio_ccs.bash
 
 
plotting_featureCounts.r
plotting_featureCounts.r
 
 
qc_results_plotting.R
qc_results_plotting.R
 
 
run_longQC.sh
run_longQC.sh
 
 
samtools_stats_pacbio.bash
samtools_stats_pacbio.bash
 
 
smrtlink_pacbio_align_hg38.bash
smrtlink_pacbio_align_hg38.bash
 
 
smrtlink_pacbio_align_merged_hg38.bash
smrtlink_pacbio_align_merged_hg38.bash
 
 
smrtlink_pacbio_align_mycoplasma.bash
smrtlink_pacbio_align_mycoplasma.bash
 
 
smrtlink_pacbio_ccs.bash
smrtlink_pacbio_ccs.bash
 
 
smrtlink_pacbio_cluster.bash
smrtlink_pacbio_cluster.bash
 
 
smrtlink_pacbio_collapse.bash
smrtlink_pacbio_collapse.bash
 
 
smrtlink_pacbio_collapse_merged_ref.bash
smrtlink_pacbio_collapse_merged_ref.bash
 
 
smrtlink_pacbio_lima.bash
smrtlink_pacbio_lima.bash
 
 
smrtlink_pacbio_merged_align_cluster_collapse.bash
smrtlink_pacbio_merged_align_cluster_collapse.bash
 
 
smrtlink_pacbio_refine.bash
smrtlink_pacbio_refine.bash
 
 
smrtlink_raw_pacbio_align_mycoplasma.bash
smrtlink_raw_pacbio_align_mycoplasma.bash
 
 
smrtlink_raw_pacbio_align_sequins.bash
smrtlink_raw_pacbio_align_sequins.bash
 
 
sqanti3_pacbio.bash
sqanti3_pacbio.bash
 
 
sqanti3_pacbio_merged.bash
sqanti3_pacbio_merged.bash
 
 
sqanti3_pacbio_merged_ref.bash
sqanti3_pacbio_merged_ref.bash
 
 
talon_all.bash
talon_all.bash
 
 

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long read benchmark project scripts

As a safe place for the scripts used in the long-read benchmarking project. Re-use of the code is at anyone's own descretion. They are written for sole individual use so may not work on every platform/system.

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A safe place for the personal scripts used in the long-read benchmarking project.

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long-read

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GPL-2.0 license
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