linzhi2013/gbseqextractor

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Python
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GNU General Publi...
Created over 6 years ago
Updated 10 months ago

linzhi2013/gbseqextractor

linzhi2013

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Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.

MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

taxonomy_ranks

To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)

msaconverter

msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (http://www.biopython.org/)

extract_codon_alignment

To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.

msa_cigars

A tool to get the CIGARs of a multiple sequence alignment.

extractfq

Extract some fastq reads from the beginning of the files

Virusfishing

Virusfishing is a virus screening pipeline for 1000 Insect Transcriptome Evolution (1KITE) project to search viruses, construct viral genomes and screen for the expressed virus genes and discover viral splicing patterns. Virusfishing also can be used in other next generation sequencing data.

wdl_dep_resolution

to reuse the existing WDL pipelines

extract_fasta_seq

To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013

bold_identification

To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)

polish_genbank

Check for the internal stop codon, then substitute the internal stop codon with NNN.