This tiny post is to celebrate my first Bioconda release, the handy n50 utility, that as the name implies calculates N50 from either FASTA or FASTQ files. The main use I did of this script was to quickly feed the output in bash scripts like:

CHECK=$(n50 contigs.fasta)

But now it has a whole range of output options including JSON, TSV, CSV and this fancy human friendly alternative:

.----------------------------------------------------------------.
| File               | Seqs   | Total bp   | N50   | min | max   |
+--------------------+--------+------------+-------+-----+-------+
| test_fasta_grep.fa |      1 |         80 |    80 |  80 |    80 |
| small_test.fa      |      6 |        130 |    65 |   4 |    65 |
| rdp_16s_v16.fa     | 13,212 | 19,098,167 | 1,467 | 320 | 2,210 |
'--------------------+--------+------------+-------+-----+-------'

How to get it

From Miniconda: Install with Conda Conda (channel only)

conda install -c bioconda n50

or with CPANminus:

cpanm Proch::N50