2760 days ago
Standardized velvet assembly report
...flatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a referenc...2759 days ago
CISA: Contig Integrator for Sequence Assembly
...zing various parameters in an assembler is often performed in order to generate the most optimal assembly. Ho...uracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for...2753 days ago
Modular, efficient and constant-memory single-cell RNA-seq preprocessing
With kallisto | bustools you can Generate a cell x gene or cell x transcript equivalence class count matrix Perform RNA velocity and single-nuclei RNA...1181 days ago
2690 days ago
splitbam: splits a BAM by chromosomes
...|stdin) Options -h help; This screen. -R (indexed reference file) REQUIRED. -u (unmapped chromosome name): default:Unmapped -e | --empty : generate EMPTY bams for chromosome hav...2678 days ago
2643 days ago
CLA: Contig-Layout-Authenticator
...ding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds. Script&nb...2612 days ago
2612 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a...2605 days ago