chiulab / SURPI-plus-dist
This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical metagenomic sequence data. Please download SURPI+ software from here.
☆35Updated 4 years ago
Related projects: ⓘ
- Workflows for metagenomic sequence data processing and analysis.☆17Updated 5 years ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated last year
- ☆21Updated 4 years ago
- Generate unique KMERs for every contig in a FASTA file☆43Updated 2 years ago
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆28Updated 6 months ago
- catalog for long-read sequencing tools☆32Updated last year
- Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.☆51Updated last month
- Error correction of ONT transcript reads☆57Updated last year
- Genome scaffolding based on HiC data in heterozygous and high ploidy genomes☆58Updated 3 years ago
- A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt☆30Updated 3 years ago
- Filter SAM file for soft and hard clipped alignments☆46Updated 3 months ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated last year
- A simple tool to calculate reads number and total base count in FASTQ file☆20Updated 5 years ago
- A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate☆31Updated 2 years ago
- ☆21Updated 5 years ago
- ☆29Updated last year
- dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…☆47Updated last year
- microRNA PREdiction From small RNA-seq data☆29Updated 6 years ago
- A program for detection of tRNA genes☆55Updated last year
- A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data☆30Updated 3 years ago
- PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics☆32Updated last year
- Metagenomics Workshop☆27Updated 7 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆41Updated 11 months ago
- Automatically exported from code.google.com/p/prottest3☆34Updated 6 years ago
- Code for running the analysis in our universe of genes project☆8Updated 5 years ago
- Pipeline for annotating genomes using long read transcriptomics data with pinfish☆27Updated 3 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆64Updated 6 years ago
- Calculates the lowest common ancestors of each query sequence in a Blast result☆31Updated 6 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆56Updated last year