Seqtk - Toolkit for processing sequences in FASTA/Q formats.seqmagick - file format conversion in Biopython in a convenient way.SeqKit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang.SeqFu - Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.RSEM - A software package for estimating gene and isoform expression levels from RNA-Seq data.Parasail - SIMD C library for global, semi-global, and local pairwise sequence alignments.POA - Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences.Octopus - A polymorphic bayesian genotyping model with wide applicability.mosdepth - fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.mergesam - Automate common SAM & BAM conversions.manta - Structural variant and indel caller for mapped sequencing data.MMseqs2 - Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.MUMmer - A system for rapidly aligning entire genomes, whether in complete or draft form.MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report.lumpy - lumpy: a general probabilistic framework for structural variant discovery.gridss - GRIDSS: the Genomic Rearrangement IDentification Software Suite.GATK - Variant Discovery in High-Throughput Sequencing Data.freebayes - Bayesian haplotype-based polymorphism discovery and genotyping.Fastx Tookit - FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities. ![]() Fastqp - FASTQ and SAM quality control using Python.FastQC - A quality control tool for high throughput sequence data.This tool is developed in C++ with multithreading supported to afford high performance. fastp - A tool designed to provide fast all-in-one preprocessing for FastQ files.DeepVariant - Deep learning-based variant caller.Delly- Structural variant discovery by integrated paired-end and split-read analysis.Cufflinks - Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.bam toolbox MtDNA:Nuclear Coverage BAM Toolbox can output the ratio of MtDNA:nuclear coverage, a proxy for mitochondrial content.bcftools - samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.Bamtools - Collection of tools for working with BAM files.BWA - Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.Bowtie 2 - An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.AfterQC - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.Fax (from U.S.): +44-1865-784-601.General Resources for Genomics Omics Contents MacVector 6.5.3 is MacOS 9 compatible and Y2K compliant.įor more information: Kevin Kendall, Engineer, Oxford Molecular Group, The Medawar Centre, Oxford Science Park, Oxford, OX4 4GA, UK. MacVector 6.5.3 also offers improved readability of text on circular feature maps and faster color printing of multiple sequence alignments. MacVector 6.5.3 also includes several other new features, including the ability to retrieve from NCBI's "Entrez" (a browser that helps researchers access information from across NCBI's integrated databases). "To this end, this release ensures that users will continue to be able to access the NCBI-based database search functions when the BLAST 1.4 servers are no longer in operation." "We understand that BLAST searches are an integral and critical operation in determining a new sequence's function within an organism," said John Devereux, president of Genetics Computer. All registered users of MacVector 6.5 will receive this latest upgrade to version 6.5.3 free of charge. Recently awarded the 1999 "Best User Interface" by Biotechnology Software & Internet Journal, MacVector 6.5.3 ensures researchers full compatibility with the National Center for Biotechnology Information's (NCBI) new BLAST 2.0 servers, which will soon replace the current BLAST 1.4 servers.īLAST, which stands for Basic Local Alignment Search Tool, is a program for comparing gene and protein sequences against others in public databases. Genetics Computer Group (Madison, WI), an Oxford Molecular company focusing on genome informatics software, has launched MacVector 6.5.3, an update to its popular sequence analysis software for Macintosh computers.
0 Comments
Leave a Reply. |