Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of cutesv

cutesv - Version update

- Python
Published by Meltpinkg 12 months ago

cutesv - Version update

  1. fix bugs in resolving reference genomes
  2. modify several dependencies and remove some useless dependencies
  3. update several evaluation scripts

- Python
Published by Meltpinkg almost 2 years ago

cutesv - Version update

  1. Speed up both SV discovery calling and force calling comprehensively.
  2. Upgrade the force-calling module.
  3. Update several functions and regulations.

- Python
Published by Meltpinkg over 2 years ago

cutesv - Version update

  1. Speed up both SV discovery calling and force calling comprehensively.
  2. Upgrade the force-calling module.
  3. Update several functions and regulations.

- Python
Published by Meltpinkg over 2 years ago

cutesv - Version update

  1. Fix the error of missing min_size parameter.
  2. Fix the missing signatures in duplication clustering.

- Python
Published by Meltpinkg almost 3 years ago

cutesv - Version update

  1. Fix several errors in signature extraction.
  2. Filter low quality reads in the statistics of reference reads.
  3. Modify the rule of merging signatures on the same read.
  4. Modify the cluster rule of insertions and deletions in force calling.

- Python
Published by Meltpinkg over 3 years ago

cutesv - Version update

  1. Fix an error in handling strand in force calling.
  2. Speed up the genotype module of discovery calling. The comparison results on various datasets are as follows.

| | cuteSV (previous) | cuteSV2 (latest) | | :------------: |:---------------:|:-------------:| | CCS | 900.37s | 261.77s | | CLR | 3620.00s | 2644.94s | | ONT | 2893.08s | 1264.26s |

- Python
Published by Meltpinkg over 3 years ago

cutesv - Version upgrade

cuteSV (v2.0.0): 1. Upgrade the force-calling module. 2. Add --remainreadsratio parameter in order to generate a highly accurate record by discarding a few signatures. 3. Fix several bugs in inversion and translocation calling. 4. Remove the redundant operations in the signature extraction and accelerate the whole analysis. 5. Streamline the translocation output when performing force-calling. 6. Modify the signature matching rule. 7. Modify the sequence of the inserted allele.

- Python
Published by tjiangHIT over 3 years ago

cutesv - v1.0.13

  1. Modify the breakpoints of alternative allele and reference allele.
  2. Fix an initialization error that will reproduce wrong diploid-assembly-based SV call.

- Python
Published by tjiangHIT about 4 years ago

cutesv - v1.0.12

cuteSV (v1.0.12): 1. Add Allele frequency (AF) info in the outputs. 2. Fix an index error when force calling BND variants. 3. Modify the parameter of --max_size and enable to report full length of SVs.

- Python
Published by tjiangHIT over 4 years ago

cutesv - cuteSV-v1.0.11

cutesv (v1.0.11): 1. Add a script for post-processing typically cuteSV callsets from assembly-based alignments to generate the diploid-assembly-based SV calls. 2. Give a wiki page for helping uses to achieve assembly-based SV calling. 3. Improve acquirement of inserted sequence in a read whose primary alignment contains hardclips. 4. Improve the performance of force calling. 5. Enable cuteSV to output allele sequences when performing force calling with the VCF generated from other callers. 6. Fix bugs to avoid the error raised by abnormal SV type. 7. Update the sort commands used in cuteSV.
8. Update the parameter of --maxsplitparts.

- Python
Published by tjiangHIT almost 5 years ago

cutesv - cuteSV-v1.0.10

cutesv (v1.0.10): 1. Fix a bug leading to calculate wrong TRA positions. 2. Add a file format conversion script that enable to transfer the vcf file to bedpe file. 3. Involve several clustering-and-refinement strategies in force calling function. 4. Assessed the performance of force calling with Giab HG002 sample datasets (including CLR, CCS, and ONT platforms).

- Python
Published by tjiangHIT about 5 years ago

cutesv - cuteSV-v1.0.9

cutesv (v1.0.9): 1. Change 0-based pos into 1-based pos in DUP in order to support bcftools conversion. 2. Correct REF and ALT fields. Adjust END value of INS to make it equal to the value of POS. 3. Improve the description of errors. 4. Add usegalaxy.eu badge. 5. Remove CHR2 and the corresponding END position on the BND call. 6. Skip generating empty signature file and rewrite the job schedule. 7. Add force calling function and enable cuteSV to perform population-based SV calling. 8. Fix several minor bugs.

- Python
Published by tjiangHIT over 5 years ago

cutesv - cuteSV-v1.0.8

cutesv (v1.0.8): 1. Rewirte the function of ins/del signatures clustering. 2. Update the recommandation parameters for different sequencing datasets. 3. Replace <DEL>/<INS> with its variant allele sequence, which needs the reference genome sequence as input. 4. Fix several bugs.

- Python
Published by tjiangHIT over 5 years ago

cutesv - cuteSV-v1.0.7

  1. Add read name list for each SV call.
  2. Fix several descriptions in VCF header field.

- Python
Published by tjiangHIT over 5 years ago

cutesv - cuteSV-v1.0.6

1.Improvement of genotyping by calculation of likelihood. 2.Add variant quality value, phred-scaled genotype likelihood and genotype quality in order to filter false positive SV or quality control. 3.Add --gt_round parameter to control the number of read scans. 4.Add variant strand of DEL/DUP/INV. 5.Fix several bugs.

- Python
Published by tjiangHIT almost 6 years ago

cutesv - cuteSV-v1.0.5

cuteSV (v1.0.5): 1.Add new options for specificly setting the threshold of deletion/insertion signals merging in the same read. The default parameters are 0 bp for deletion and 100 bp for insertion. 2.Remove parameter --merge_threshold. 3.Fix bugs in inversion and translocation calling. 4.Add new option for specificly setting the maximum size of SV to be discovered. The default value is 100,000 bp.

- Python
Published by tjiangHIT almost 6 years ago

cutesv - cuteSV-v1.0.4

1.Add a new option for specificly setting the threshold of SV signals merging in the same read. The default parameter is 500 bp. You can reduce it for high-quality sequencing datasets like PacBio HiFi (CCS). 2.Make the genotyping function optional. 3.Enable users to set the threshold of SV allele frequency of homozygous/heterozygous. 4.Update the description of recommendation parameters in processing ONT data.

- Python
Published by tjiangHIT about 6 years ago

cutesv - cuteSV-v1.0.3

1.Refine the genotyping model. 2.Adjust the threshold value of heterozygosis alleles.

- Python
Published by tjiangHIT about 6 years ago

cutesv - cuteSV-v1.0.2

1.Improve the genotyping performance and enable it to be default option. 2.Make the description of parameters better. 3.Modify the header description of vcf file. 4.Add two new indicators, i.e., BREAKPOINTSTD and SVLENSTD, to further characterise deletion and insertion. 5.Remove a few redundant functions which will reduce code readability.

- Python
Published by tjiangHIT over 6 years ago

cutesv -

- Python
Published by tjiangHIT over 6 years ago