Pinned Repositories
16S_Tutorial
2014-5-metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
2016
Materials prepared by the instructors of the #NGSchool2016
2016-tutorials
repo for 2016 EDAMAME tutorials
2017
Materials used during #NGSchool2017
AliTV
Visualize whole genome alignments as linear maps
angus
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
Annocript
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript
apt-cyg
Apt-cyg, an apt-get like tool for Cygwin
LS-BSR
Large scale Blast Score Ratio (BSR) analysis
palc's Repositories
palc/LS-BSR
Large scale Blast Score Ratio (BSR) analysis
palc/2017
Materials used during #NGSchool2017
palc/angus
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
palc/bac-genomics-scripts
Collection of scripts for bacterial genomics
palc/BacMet-database
palc/bioconda-recipes
Conda recipes for the bioconda channel.
palc/Bioinformatics_scripts-1
Scripts UBC
palc/blasr
BLASR: The PacBio® long read aligner
palc/ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
palc/COGmapper
This is a pipeline for finding out the COG (Cluster of Orthologous Groups) distribution for a list of bacterial genomes.
palc/fastqe
FASTQ sequence quality visualisation with Emoji
palc/FuzzyID2
FuzzyID2: A software package for large dataset species identification via barcoding and metabarcoding using Hidden Markov Models and fuzzy set methods
palc/gawn
GAWN - Genome Annotation Without Nightmares
palc/gff3toembl
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
palc/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
palc/HPViewer
palc/map_viruses
Align short reads against viral genomes in protein space
palc/metabarcoding_workflow
R scripts for metabarcoding analysis for invertebrate COI amplicon data
palc/MetBaN
Automated pipeline for metabarcoding data using taxonomical/phylogenetical classification of organisms
palc/MicrobialGenomeMetagenomeCourse
Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017
palc/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
palc/ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
palc/pyfaidx
Efficient pythonic random access to fasta subsequences
palc/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
palc/Scripts
Scripts developped over time and (sometimes) still usefull
palc/Sequence-scripts
Random utility scripts for genomics data
palc/stacks_workflow
RADseq workflow using STACKS
palc/taxonomy_conversion
scripts to convert qiime taxonomy format to RDP format
palc/Unicycler
hybrid assembly pipeline for bacterial genomes
palc/VirFinder
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data