Biotite: A general framework for computational biology
...and structural data analysis respectively, database downloads files from the other databases suc...focuses on working with sequence and structure data and supports various file formats and analysis and mani...1993 days ago
1968 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage...V]positive_seq negative_seq positional arguments:positive_seq the fasta file for the positive sequencesneg...1966 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, deduplic...1959 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
...o assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected...1955 days ago
DISTRUCT: a program for the graphical display of population structure
...load software note from Molecular Ecology Notes 4: 137-138 (2004)] To use the UNIX versions, unzip and untar the files in an appropriate directory using gunzip filename.tar.gz; tar xvf filename....1895 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bi...1872 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...It can either read reference genomes from FASTA files or simulate new ones. Genomi...tistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations&...licates. All outputs can be written to standard file formats. A swift, versatile...1773 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bi...1680 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
...25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of...1659 days ago