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/Integron_Finder
Find integrons in DNA sequences
palc/multi-metagenome
palc/biostar-tutorials
Code for biostar tutorials - mostly R and Perl
palc/oneliners
Useful bash one-liners for bioinformatics.
palc/awesome-public-datasets
An awesome list of high-quality datasets in public domains (on-going).
palc/microbiome-tools
For tool creators to share their inventions that analyze, visualize, and make meaning of microbiome data.
palc/blastdbget
Download Blast databases from ftp.ncbi.nlm.nih.gov/blast/db, validate, and extract.
palc/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
palc/sequence_processing
some scripts to process fasta and fastq sequences
palc/chommeta
scripts to reproduce the analysis and figures from Hacquard et al., Cell Host and Microbe, 2015
palc/Scaffolder-evaluation
Wrapper scripts to run genome assembly scaffolding tools and scripts to analyse the output for accuracy.
palc/co-occurrence
R scripts for performing co-occurrence analyses
palc/samtools_primer
SAMtools: A Primer
palc/linked-selection
palc/SeqFindR
A tool to easily create informative genomic feature plots
palc/epicPCR
Scripts to parse sequence data from Emulsion, Paired Isolation, and Concatenation PCR
palc/Jellyfish
A fast multi-threaded k-mer counter
palc/2014-5-metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
palc/ngs_workshop
A Next Generation Sequencing (NGS) Workshop developed by Bioplatforms Australia (BPA), CSIRO, EMBL-Australia and the EBI.
palc/MLST
palc/Mannotator
Microbial annotation pipeline - in progress
palc/SpeciesFinder
Bacterial species prediction from NGS reads, contains or whole genomes.