{"repo":"nf-core/viralmetagenome","free":true,"listed":false,"github":"https://github.com/nf-core/viralmetagenome","clone":"git clone https://github.com/nf-core/viralmetagenome.git","description":"A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.","language":"Nextflow","stars":40,"topics":["epidemiology","fastq","nextflow","ngs","virology","virus-genomes","viral-metagenomics","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/viralmetagenome is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture. [!NOTE] - indicates the need to choose a tool - & indicate that output of tools can be combined and run in parallel. 1. Read QC ( FastQC ) 2. Performs optional read pre-processing - Adapter trimming( fastp , Trimmomatic ) - Read UMI deduplication ( HUMID ) - Low complexity and quality filtering ( bbduk , prinseq++ ) - Host-read removal ( Kraken2 ) 3. Metagenomic diversity mapping ( Kraken2 , Bracken Kaiju ) 4. Denovo assembly ( SPAdes , TRINITY , megahit ), combine contigs. 5. [Optional] Extend the contigs with sspace basic and filter with prinseq++ 6. [Optional] Map reads to contigs for coverage estimation ( Bowtie2 , BWA-MEM2 ) 7. [Optional] Contig reference identification ( blastn ), the top 5 hits for every contig are considered for scaffolding 8. [Optional] Precluster contigs on taxonomy classification with Kraken2 and/or Kaiju 9. Cluster contigs (or every taxonomic bin) with any of the following tools: CD-HIT-EST , vsearch , mmseqs-linclust , mmseqs-cluster , vRhyme or Mash with Clusty 10. [Optional] Remove clusters with low read coverage. bin/extract clusters.py 11. Scaffolding of contigs to centroid ( Minimap2 , iVar-consensus ) 12. [Optional] Select best reference from --mapping constraints : ( Mash sketch , Mash screen )","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/viralmetagenome/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}