Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genom...1992 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...s from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequenc...in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index tha...1986 days ago
MCAT: Motif Combining and Association Tool
...][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional arguments:positive_seq the fasta file for the positive sequencesnegative_seq the fasta file for the negative sequences1980 days ago
gVolante: Completeness Assessment of Genome/Transcriptome Sequences
A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section1980 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorith...1980 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation a...1979 days ago
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, deduplicat...1973 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts an...datasets containing non-functional sequences (pseudogenes) without disrupt...ted frameshifts in public database sequences and in aligning next-generati...1944 days ago
SDA: Long-read sequence and assembly of segmental duplications
...lication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repuls...1929 days ago
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