telatin/learn_bash

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Created almost 7 years ago
Updated over 1 year ago

telatin/learn_bash

telatin

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Toy files and training material to introduce Linux to molecular biologists

seqfu2

🚀 seqfu - Sequece Fastx Utilities

bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊

covtobed

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

gan

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

nextflow-example

A simple DSL2 workflow: tutorial

covtools

getreads

porfast

⚡pORFast - Paired-end ORF Fast extraction

qax

Qiime2 Artifact eXtractor

cdhit-parser

singularities

Scripts and notes for singularity containers used for bioinformatics analyses

cleanup

Nextflow pipeline to preprocess metagenomics reads

FASTX-Reader

[FASTX::Reader] Perl module to parse FASTQ files, without depending on BioPerl

nextseq500-tools

Tools to deal with Illumina NextSeq500 sequences

nim-for-bioinformatics

Notes on the Nim programming language, with specific examples for bioinformatic applications

nim-stuff

vsearch_example

An example of 16S analysis using VSEARCH

bioinfo

Misc scripts for routine bioinformatics tasks. Plus some Perl modules.

learnperl

Scripts used for Bash/Perl training sessions

tii

Like 'tee', but for PasteBin.com

FASTX-Abi

Perl module to convert Sanger traces (chromatograms) to FASTQ

lotus-tutorial

Tutorial on 16S analysis using the Lotus pipeline

qiime2tools

Repository of utilities for Qiime2. Experimental

factotus

The OTUs Factotum

nf-core-virome

proch-n50

Perl Module and Utility to calculate N50

scampi

Archived PhD thesis material from 2012

praken

Peptide k-mer analysis

amplicorius

AmpliCoriuS - Amplicon Core Scripts

ml-workshop-2023

Machine Learning with Python

Jupyter Notebook

telatin.github.io