Pinned Repositories
bold_identification
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
extract_codon_alignment
To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
extract_fasta_seq
To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013
extractfq
Extract some fastq reads from the beginning of the files
gbseqextractor
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
msa_cigars
A tool to get the CIGARs of a multiple sequence alignment.
msaconverter
msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (http://www.biopython.org/)
taxonomy_ranks
To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)
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.
linzhi2013's Repositories
linzhi2013/MitoZ
MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
linzhi2013/taxonomy_ranks
To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)
linzhi2013/gbseqextractor
Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
linzhi2013/msaconverter
msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (http://www.biopython.org/)
linzhi2013/extract_codon_alignment
To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
linzhi2013/msa_cigars
A tool to get the CIGARs of a multiple sequence alignment.
linzhi2013/bold_identification
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
linzhi2013/extract_fasta_seq
To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013
linzhi2013/polish_genbank
Check for the internal stop codon, then substitute the internal stop codon with NNN.
linzhi2013/specimen_bioseq_system
The Specimen Bioseq Information Managment System
linzhi2013/academic-kickstart
linzhi2013/atgcN_count
To stat the counts of each base in a fasta file.
linzhi2013/batch_tar
To tar (and compress) files or directories in batch mode.
linzhi2013/bioconda-recipes
Conda recipes for the bioconda channel.
linzhi2013/books-1
我读过的书。嘿嘿，分享给你。
linzhi2013/breakSeqInNs_then_translate
Filter the sequences by translating the protein coding genes (PCGs) with proper genetic code table, if one of the PCGs has interal stop codon, filter out this sequence.
linzhi2013/busco_process_scripts
linzhi2013/cigar_coordinates
To get the coordinates of a given CIGAR string.
linzhi2013/easy-algorithm-interview-and-practice
linzhi2013/extract_specific_lines
To extract specific lines which maps the query ids (of the query file) from the subject file.
linzhi2013/extract_specific_sites_from_msa
To extract some sites (or codon) from a multiple sequence alignment
linzhi2013/find_longest_transcripts
To find out the longest transcripts/proteins
linzhi2013/group_genetic_distance
To derive within- and between-groups genetic distance based on pairwise genetic distance matrix
linzhi2013/lcwgs-guide-tutorial
linzhi2013/lcwgs-simulation
linzhi2013/Machine-learning-learning-notes
周志华《机器学习》又称西瓜书是一本较为全面的书籍，书中详细介绍了机器学习领域不同类型的算法(例如：监督学习、无监督学习、半监督学习、强化学习、集成降维、特征选择等)，记录了本人在学习过程中的理解思路与扩展知识点，希望对新人阅读西瓜书有所帮助！
linzhi2013/mglcmdtools
`mglcmdtools` is a collection of common cmd tools intended to be used in Python3 scripts. By Guanliang MENG, see https://github.com/linzhi2013/mglcmdtools.
linzhi2013/ntJoin
🔗Genome assembly scaffolder using minimizer graphs
linzhi2013/ParallelTask
A simple and lightweight parallel task engine
linzhi2013/physalia-lcwgs
Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 11-14, 2021