https://github.com/applicativesystem/pacbio-nanopore-polyatgc-remove

polyATGC pacbio/oxford nanopore estimator
https://github.com/applicativesystem/pacbio-nanopore-polyatgc-remove

bioinformatics genome-analysis genome-annotation pacbio-data pacbio-hifi-sequencing-reads pacbio-sequencing pacbiohifi

Last synced: 7 months ago
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polyATGC pacbio/oxford nanopore estimator

• Host: GitHub
• URL: https://github.com/applicativesystem/pacbio-nanopore-polyatgc-remove
• Owner: applicativesystem
• License: mit
• Created: 2024-08-20T19:09:34.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-08-20T19:47:45.000Z (10 months ago)
• Last Synced: 2024-11-10T20:18:16.930Z (8 months ago)
• Topics: bioinformatics, genome-analysis, genome-annotation, pacbio-data, pacbio-hifi-sequencing-reads, pacbio-sequencing, pacbiohifi
• Language: Python
• Homepage:
• Size: 1.95 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# pacbio-nanopore-polyATGC-trimmer

- A regular expression based polyATGC trimmer from the long reads or the fastq reads extremely fast and returns a fasta and also a dataframe for the sequence classification and this takes the current as 10 continuous bases.

- A sample on how to run the code is given below. if you are using the long reads for machine learning then it directly returns a dataframe for ingestion to machine leaning.

```

longreadpolyATGCtrimmer("/Users/gauravsablok/Desktop/CodeCheck/fasta_sample_datasets/test_sample_short.fasta",

                              polyATGCstretch_type="G")

	ids	sequences	stretch_count	trimmed_sequences_new

0	>1	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

1	>2	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

2	>3	GCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...	[27, 30]	GCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...

3	>4	CGAAAATTACTTCGGTACAATGCTTGTATACATGGGCAAAGCACAC...	[33, 36]	CGAAAATTACTTCGGTACAATGCTTGTATACATCAAAGCACACGGT...

```

Gaurav Sablok \

Academic Staff Member \

University of Potsdam \

Potsdam,Germany