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/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/extractfq
Extract some fastq reads from the beginning of the files
linzhi2013/wdl_dep_resolution
to reuse the existing WDL pipelines
linzhi2013/batch-run-cmd
To run commands line by line, and check each exit status.
linzhi2013/bioinfo_versatiles
a set of frequently used perl programs that faciliate bioinformatics analysis jobs, which may be very helpful especially for the new bioinformaticians
linzhi2013/biosoft-notes
some notes about some biosofts
linzhi2013/books
常用书籍
linzhi2013/clusterProfiler
:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters
linzhi2013/common-conda-enviroments
some daily used conda environments
linzhi2013/CourseComparativeMethods
Examples of application of comparative methods in R
linzhi2013/DeepSeqAnalysis
Course materials for a graduate class in applied bioinformatics for biologists
linzhi2013/demo-source-protect
linzhi2013/genomics_general
General tools for genomic analyses.
linzhi2013/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
linzhi2013/jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
linzhi2013/macrophy_course
Macroevolution & Phylogenetics Course
linzhi2013/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
linzhi2013/pandas_answered
pandas tips
linzhi2013/pgmtdna
:evergreen_tree: Annotate the mitochondrial genome of white spruce (Picea glauca)
linzhi2013/Python-3-Object-Oriented-Programming-Third-Edition
Python 3 Object-Oriented Programming – Third Edition, published by Packt
linzhi2013/redundans
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
linzhi2013/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
linzhi2013/Sniffles
Structural variation caller using third generation sequencing
linzhi2013/SOAPBarcode
SOAPBarcode: Assemble standard COI barcode region with two libraries, of which one is full length, another is shotgun. https://doi.org/10.1111/2041-210X.12120
linzhi2013/SQANTI2
Private repo for Liz's modified SQANTI
linzhi2013/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
linzhi2013/tracy
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
linzhi2013/training-material
A collection of Galaxy-related training material
linzhi2013/tutorials-1
Tutorials on phylogenomic analyses for the ForBio Phylogenomics course
linzhi2013/VESPA
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses