The typical segment length is determined by finding the median length of the segment/subject reference sequences whose contig alignments have the highest bitscore. Segment_cov : the number of sequenced bases in the consensus sequence divided by the typical length of this genome segment (as a percentage). Sequenced_bases : the number of nucleotide positions in the consensus sequence with sufficient depth of coverage (set by -D argument) and a succesful base call (e.g. Seq_length : the length (in nucleotides) of the consensus sequence generated by FluViewer F 0xXX only report alignment records where the. f 0xXX only report alignment records where the specified flags are all set (are all 1) you can provide the flags in decimal, or as here as hexadecimal. Mapped reads : the number of sequencing reads mapped to this segment The most common samtools view filtering options are: -q N only report alignment records with mapping quality of at least N ( > N ). This is a good way to remove low quality reads, or make a BAM file restricted to a single chromosome. Subtype : HA or NA subtype ("none" for internal segments) bam files - they can be converted into a non-binary format ( SAM format specification here) and can also be ordered and sorted based on the quality of the alignment. Segment : influenza A virus genome segment (PB2, PB1, PA, HA, NP, NA, M, NS) The report TSV file contains the following columns:Ĭonsensus_seq : the name of the consensus sequence described by this row Headers in the FASTA file have the following format: >output_name_unique_sequence_number|segment|subject A report TSV file describing segment, subtype, and sequencing metrics for each consensus sequence.A sorted BAM file with reads mapped to either the choosen reference sequences (align mode) or the assembled contigs (assembly mode).A FASTA file containing consensus sequences for influenza A virus genome segments.Headers for these sequences must be formatted and annotated as follows: >unique_id|strain_name|segment|subtypeįor example: >MF599463|A/swine/Kansas/A01378028/2017|HA|H3 g : Set this flag to deactivate garbage collection and retain intermediate files FluViewer DatabaseįluViewer requires a curated FASTA file "database" of influenza A virus reference sequences. i : Minimum nucleotide sequence identity between database reference sequence and contig (percentage, default = 95) c : Minimum coverage of database reference sequence by contig (percentage, default = 25) q : Minimum PHRED score for base quality and mapping quality (default = 30) D : Minimum read depth for base calling (default = 20) m : FluViewer run mode (align or assemble) o : output name (creates directory with this name for output, includes this name in output files, and in consensus sequence headers) d : path to FASTA file containing FluViewer database (details below) r : path to FASTQ file containing reverse reads f : path to FASTQ file containing forward reads Custom DBs can be created and used as well (instructions below). Download and unzip the default FluViewer DB (FluViewer_db.fa.gz) from this repository.Once the dependencies have been installed, install the latest FluViewer release via PyPI:.FluViewer requires the following dependencies, and it is recommended to install them in a FluViewer virtual environment (indicated versions were tested, but later versions can likely be substituted):. These old versions remain available from the Sourceforge samtools project.A tool for generating influenza A virus genome sequences from FASTQ data Installation Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed Your specified prefix, so you may wish to add this directory to your $PATH: export PATH =/where/to/install/bin: $PATH # for sh or bash users setenv PATH /where/to/install/bin:$PATH # for csh users Historical SAMtools/BCFtools 0.1.x releases The executable programs will be installed to a bin subdirectory under See INSTALL in each of the source directories for further details. Building and installingīuilding each desired package from source is very simple: cd samtools-1.x # and similarly for bcftools and htslib New releases are announced on the samtools mailing lists and by Twitter. Or see the additional instructions in INSTALL to install them from a So you may also want to build and install HTSlib to get these utilities, HTSlib also provides the bgzip, htsfile, and tabix utilities, If you are writing your own programs against the HTSlib API. HTSlib is also distributed as a separate package which can be installed The code uses HTSlib internally, but these source packages contain their ownĬopies of htslib so they can be built independently. SAMtools and BCFtools are distributed as individual packages.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |