sheetvef.blogg.se - Samtools get consensus sequences

#Samtools get consensus sequences install#
#Samtools get consensus sequences download#

to split a large fasta file into several parts of same number of sequences split the large file 'uniref100.fasta' into 8 parts. The typical segment length is determined by finding the median length of the segment/subject reference sequences whose contig alignments have the highest bitscore. tail-n + 1001 largefile.txt > part2.txt get all lines starting from lines 1001 to end of file. 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) Samtools is designed to work on a stream. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. The report TSV file contains the following columns:Ĭonsensus_seq : the name of the consensus sequence described by this row Samtools is a set of utilities that manipulate alignments in the BAM format. 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.

via bcftools consensus: samtools mpileup -uf ref.fa aln.bam bcftools call -mv -Oz -o tabix cat ref.fa bcftools consensus > cns.

via vcf2fq: samtools mpileup -uf ref.fa aln.bam bcftools call -c vcf2fq > cns.fq. A sorted BAM file with reads mapped to either the choosen reference sequences (align mode) or the assembled contigs (assembly mode) And then I found it seems two ways to generate the consensus sequence.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).

#Samtools get consensus sequences download#

Download and unzip the default FluViewer DB (FluViewer_db.fa.gz) from this repository.

#Samtools get consensus sequences install#

Once the dependencies have been installed, install the latest FluViewer release via PyPI: Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA.

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):.

The mean read depth, the breadth of coverage of the reference genome, and the proportion of the reads that mapped to the reference genome can be obtained from a BAM file using the combination of awk, and the SAMtools 1.3.1 utilities depth and flagstat.A tool for generating influenza A virus genome sequences from FASTQ data Installation The alignment section, on the other hand, has 11 mandatory fields, as well as a variable number of optional fields: Col Unordered multiple lines are text comment.

The order of lines defines the alignment sorting group. OPTIONS -a, -assembly STR Specify the assembly for the AS tag. The table below describes the available predefined tags in the header section of a SAM file: header line. DESCRIPTION Create a sequence dictionary file from a fasta file. Header section is denoted by the character followed by one of the two-letter header record type codes.