SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplicati...1930 days ago
1930 days ago
iRNAD: a computational tool for identifying D modification sites in RNA sequence
iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. http://lin-group.cn/server/iRNAD/1814 days ago
simuG: a general-purpose genome simulator
...ng genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Del...1618 days ago
Kevler: Reference-free variant discovery in large eukaryotic genomes
...novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/de...1557 days ago
mutatrix: a population genome simulator which generates simulated genomes.
genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta1557 days ago
NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various loca...1459 days ago
HS3D: Homo Sapiens Splice Sites Dataset
...d (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleo...1421 days ago
1414 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact am...1270 days ago