Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignm...2198 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
...pecific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quive...2224 days ago
CGView - Circular Genome Viewer
...ans of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView...2197 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output...s, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports...2189 days ago
2185 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...alyse jellyfish hashes or sequence files (fasta or fastq) using kmer...k-mer occurrences from a sequence file. Adds metadata in output for...rs between two (or three) sequence files or hashes. sect: SEquence C...filtering k-mer hashes and FastQ/A files: kmer: Produces a k-mer h...2033 days ago
2150 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
...alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser co...2150 days ago
2149 days ago
SimLoRD: A read simulator for third generation sequencing reads
...enerated reference sequence. The reference can be read from a FASTA file or randomly generated with a...distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling f...2134 days ago