![]() ![]() Fields that are different across replicates(fields apart from REGION, POS, REF, ALT) will have the filename added as a suffix. This intersection will filter out any SNVs that do not pass the filters(in the variant calling step) in all the replicates. tsv files) called from any number of replicates. Under the hood, iVar calls an Awk script to get an intersection of variants(in. This was tested in samtools 1.7 and 1.8.įilter variants across replicates with iVar When a reference sequence is supplied, the quality of the reference base is reduced to 0 (ASCII: !) in the mpileup output. Note: Please use the -B options with samtools mpileup to call variants and generate consensus. To sort and index an aligned BAM file, the following command can be used, If after trimming, the length of the read is greater than the minimum length specified(Default: 30), the read is written to the new trimmed BAM file. The windows slides from the 5' end to the 3' end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped. To do the quality trimming, iVar uses a sliding window approach(Default: 4). Following this, the reads are trimmed based on a quality threshold(Default: 20). IVar uses primer positions supplied in a BED file to soft clip primer sequences from an aligned and sorted BAM file. To view detailed usage for each command type ivar Note : Commands maked (EXPERIMENTAL) are still under active development. (EXPERIMENTAL) Trim adapter sequences from reads The typical segment length is determined by finding the median length of the segment/subject reference sequences whose contig alignments have the highest bitscore.Detect primer mismatches and get primer indices for the amplicon to be masked 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 Mapped reads : the number of sequencing reads mapped to this segment Subtype : HA or NA subtype ("none" for internal segments) 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):.A tool for generating influenza A virus genome sequences from FASTQ data Installation ![]()
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