{"repo":"nf-core/bactmap","free":true,"listed":false,"github":"https://github.com/nf-core/bactmap","clone":"git clone https://github.com/nf-core/bactmap.git","description":"A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences","language":"Nextflow","stars":67,"topics":["nf-core","nextflow","workflow","pipeline","bacteria","bacterial","bacterial-genome-analysis","phylogeny","mapping","genomics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/bactmap is a bioinformatics best-practice analysis pipeline for mapping short (Illumina) and long reads (Oxford Nanopore) from bacterial WGS to a reference sequence, creating filtered VCF files and making pseudogenomes based on high quality positions in the VCF files. Pipeline summary 1. Index reference fasta file (short-read: BWA index or Bowtie2 build ; long-read: minimap2 index ) 2. Read QC ( FastQC or falco as an alternative option) 3. Calculate fastq summary statistics ( fastq-scan ) 4. Perform read pre-processing (optional) - Adapter clipping and merging (short-read: fastp or AdapterRemoval2 ; long-read: porechop or Porechop ABI ) - Quality filtering (long-read: Filtlong ), Nanoq - Run merging ( cat ) 5. Downsample fastq files (optional) ( Rasusa ) 6. Summarise read statistics pre- and post-processing and subsampling ( read stats ) 7. Variant calling - Map reads to reference (short-read: BWA-MEM2 or Bowtie2 ; long-read: minimap2 ) - Sort and index alignments ( SAMtools view/sort ) - Summarise alignment statistics ( SAMtools stats ) - Call variants (short-read: FreeBayes ; long-read: Clair3 ) - Filter variants ( BCFtools filter ) - Summarise variant statistics ( BCFtools stats ) - Convert filtered bcf to pseudogenome fasta ( BCFtools consensus and BEDtools ) - Summarise mapping statistics ( seqtk ) 8. Create alignment from pseudogenomes by concatenating fasta files having first checked that the sample sequences are high quality ( alignpseudogenomes )","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/bactmap/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."}