Since 0.7.11, precompiled binary for x86_64-linux is available inbwakit. In addition to BWA, this self-consistent package also comes with bwa-associated and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs, adapter triming, duplicate marking, HLA typing and associated...
1) using bioconda: conda install -c bioconda seqtk, 2) using brew on a MAC: brew install seqtk, and 3) source code: obtain source code from the GitHub repository and compile it.The following examples explains how to use seqtk subseq to extract the sequences from FASTA/FASTQ files....
Format: FASTQ (default) or FASTA Basecall-anchored modified base scores are also available in hts-spec BAM format tags (--outputs mod_basecalls). Mappings Format: SAM, BAM (default), or CRAM A tab-separated mapping text summary is also produced including per-read alignment statistics. ...
A function to extract pair end reads from the bam file generated with subread functionRaffaele A Calogero
A sorted bam fileprocess_bam(bamfile, threads) A standard fastq fileprocess_fastq_plain(fastqfile, 'threads') A fastq file with metadata from MinKNOW or Albacoreprocess_fastq_rich(fastqfile) A sequencing_summary file generated by Albacoreprocess_summary(sequencing_summary.txt, 'readtype') ...
bwa mem -5SP contigs.fasta.gz hic_paired.fastq.gz | \ samtools view -F 0x904 -bS - | \ samtools sort -o hic2ctg.bam - bin3C analysis We have split bin3C into two primary stages. mkmap: Create a contact map cluster: Clustering the contact map (genome binning) 4. Create a conta...
Format: FASTQ (default) or FASTA Basecall-anchored modified base scores are also available in hts-spec BAM format tags (--outputs mod_basecalls). Mappings Format: SAM, BAM (default), or CRAM A tab-separated mapping text summary is also produced including per-read alignment statistics. ...
FastQC (Version 0.12.0) was used for quality control of the high-throughput sequencing data (FASTQ files) from the CTRL, PRRSV, and PRRSV+CS samples. Trimmomatic (version 0.32) was employed to trim, crop, and remove adapters from the Illumina FASTQ data, facilitating downstream analysis. The...