{"repo":"nf-core/proteinfamilies","free":true,"listed":false,"github":"https://github.com/nf-core/proteinfamilies","clone":"git clone https://github.com/nf-core/proteinfamilies.git","description":"Generation and updating of protein families","language":"Nextflow","stars":23,"topics":["bioinformatics","metagenomics","nextflow","nf-core","pipeline","protein-families","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/proteinfamilies is a bioinformatics pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hidden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits. Check quality and pre-process Generate input amino acid sequence statistics with ( SeqFu ) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as / , and remove duplicate sequences) with ( SeqKit ) Create families 1. Cluster sequences ( MMseqs2 ) 2. Perform multiple sequence alignment (MSA) ( FAMSA or mafft ) 3. Optionally, clip gap parts of the MSA ( ClipKIT ) 4. Generate family HMMs and fish additional sequences into the family ( hmmer ) 5. Optionally, remove redundant and/or merge similar families by comparing family representative sequences against family models with ( hmmer ) 6. Optionally, from the remaining families, remove in-family redundant sequences by strictly clustering with ( MMseqs2 ) and discarding non-cluster representatives 7. If in-family redundancy was not removed, reformat the .sto full MSAs to .fas , for downstream analyses compatibility, with ( HH-suite3 ) 8. Op","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/proteinfamilies/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."}