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.
☆40Updated 5 years ago
Alternatives and similar repositories for SURPI-plus-dist:
Users that are interested in SURPI-plus-dist are comparing it to the libraries listed below
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- catalog for long-read sequencing tools☆32Updated 2 years ago
- Generate unique KMERs for every contig in a FASTA file☆47Updated 2 years ago
- ☆81Updated last year
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- Workflows for metagenomic sequence data processing and analysis.☆17Updated 5 years ago
- A reference viral database (RVDB)☆26Updated 6 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- ☆22Updated 5 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆66Updated 7 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- Filter SAM file for soft and hard clipped alignments☆46Updated 10 months ago
- tools for assessing the accuracy of genome assemblies☆34Updated 11 months ago
- Metagenomics Workshop☆28Updated 8 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆56Updated 4 years ago
- Automatically exported from code.google.com/p/prottest3☆36Updated 7 years ago
- Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.☆23Updated this week
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆31Updated last year
- dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…☆54Updated 2 years ago
- ☆29Updated 4 years ago
- A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data☆30Updated 3 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆56Updated 2 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆38Updated 2 years ago
- ☆12Updated 5 years ago
- Splitting of sequence reads by internal adapter sequence search☆51Updated last year
- Pangenome analysis of eukaryotes.☆18Updated 4 years ago
- ☆25Updated 3 years ago