Lighter
Lighter copied to clipboard
mourisl
Fast and memory-efficient sequencing error corrector
Hi, I sequenced a genome and I got 16 paired-end libraries. To test the speed of the program, I picked on library ~11 Gb each .gz file, and used the...
I installed lighter 1.1.1 on MacOS 10.12.4 via homebrew and it repeatedly stalled after the 'storing trusted kmers' until I killed it after 10 minutes of 0% CPU usage. It...
Hi @mourisl, It was exciting to meet you at CSHL and I appreciate that you took some time to implement the feature we discussed. I gave it a try this...
Today I upgraded from lighter 1.0.7 to 1.1.1 and I first noticed a problem when 1.1.1 was outputting different number of reads in the two output files, and then noticed...
Hello, I'm not sure that Github issue is the best place for this, but it is the suggested channel for support so will give it a go. I had some...
The number of reads is calculated by dividing the total number of lines by 4, but the program doesn't check if the total number of lines is a multiple of...
It seems like Lighter just checks if the first character of the file is '@' to consider it valid. For example, this input file (test.fq) was considered correct: @IRIS:7:1:17:394#0/1 GTCAGGACAAGAAAGACAANTCCAATTNACATTATG...
In your experience, what Bloom filter A error rate is achievable - 0.05, more, less? Should I attempt to optimize parameters such that error rate is minimized - if so,...
I'm trying to run this on my computer with a large FASTQ input file, and am running it as a subprocess in Python: # # Set the desired parameters kmer_size...
