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extract_fasta_seq

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

extract_specific_lines

To extract specific lines which maps the query ids (of the query file) from the subject file.

extract_specific_sites_from_msa

To extract some sites (or codon) from a multiple sequence alignment

find_longest_transcripts

To find out the longest transcripts/proteins

gag

Generates an NCBI .tbl file of annotations on a genome.

gbseqextractor

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

genomics_general

General tools for genomic analyses.

group_genetic_distance

To derive within- and between-groups genetic distance based on pairwise genetic distance matrix

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

introduction-to-algorithms-clrs

Introduction to Algorithms

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

jekyll_demo

jupyter

Jupyter metapackage for installation, docs and chat

lcwgs-guide-tutorial

lcwgs-simulation

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！

macrophy_course

Macroevolution & Phylogenetics Course

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.

mitoz

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

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

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/)

ntjoin

🔗Genome assembly scaffolder using minimizer graphs

orthomcl-docker

An OrthoMCL setup in a docker image

pandas_answered

pandas tips

paper-luo2012

Genome assembly pipelines from Luo et al., (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18

paralleltask

A simple and lightweight parallel task engine

pgmtdna

:evergreen_tree: Annotate the mitochondrial genome of white spruce (Picea glauca)

physalia-lcwgs

Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 11-14, 2021

polish_genbank

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