DendroPy: a Python library for phylogenetic computing
...ees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for...2201 days ago
2190 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...eatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statis...2160 days ago
2171 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...enomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (wi...2134 days ago
2131 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...AT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts....profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta coverage output coverage from...1979 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
...organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFinisher.jar \ -i target_contigs.fasta \ -ds alternative_assemblies.fasta -ref reference.fasta \...2107 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
...FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command....2083 days ago
SimLoRD: A read simulator for third generation sequencing reads
...error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference can be read from a FASTA file or randomly generated wi...2080 days ago