Linux command line exercises for NGS data processing
The purpose of this tutorial is to introduce students to the frequently used tools...red files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing in...2867 days ago
Fancy Oneliner for Bioinformatics !!
This webpage lists some of the one-liners that we frequently use in metagenomic ana...re in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are...2852 days ago
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad an...2358 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, w...2130 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertio...peed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Sn...2018 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for p...long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple...2061 days ago
2025 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amp...volutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swar...1994 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
UPhO finds orthologs with and without inparalogs from input gene family trees. Refe...ers can be defined. Examples of trees to test UPhO are provided in the TestData folder.1931 days ago